ActinoBase - User contributions [en-gb]

Teaching and learning

2021-11-18T12:39:26Z

Nelly:

=Teaching and Learning=

This is the hub for #ActinoBase teaching and learning resources: educational content, outreach, and more! We welcome contributions from the community, so please [[Admin contact page|contact]] us with any suggestions or if you would like to contribute content to these pages.

==Practical protocols (undergrad labs)==

==Bioinformatics ==
*A practical lesson on [https://carpentries-incubator.github.io/metagenomics-workshop/ Metagenomics].
*R, python, Linux, Git and other lessons at [https://software-carpentry.org/lessons/ Software Carpentry].

==Undergraduate student projects==

*[https://seaphages.org/ SEA-PHAGES], an HHMI undergraduate course featuring the discovery and isolation of actinobacteriophages
*[https://www.strath.ac.uk/viprojects/drugdiscovery/ the Strathclyde VIP Drug Discovery Project], using hyperspectral imaging to screen for novel antibiotic producers

==Spotlight: teaching antibiotics & AMR==

Are you looking for videos to use in your courses, inspiration for classroom or workshop activities, or other resources to help you with your teaching? Please check out our collection of [[Teaching and Learning Resources: Antibiotics and AMR]].

==Other teaching and learning resources==
*[https://microbiologyonline.org/teachers Microbiology Society resources for teachers]
*[https://microbiologyonline.org/students Microbiology Society resources for students]
*[https://www.asmscience.org/VisualLibrary the American Society for Microbiology's resource library]
*[https://www.asmscience.org/content/journal/jmbe Journal of Microbiology and Biology Education]
*[https://schaechter.asmblog.org/schaechter/teachers-corner-1/ Small Things Considered: Teacher's Corner]
*[http://www.actino.jp/index-e.html]

=Outreach=
[https://www.uea.ac.uk/research/explore-uea-research/antibiotic-hunters Antibiotic Hunters]: Huge congratulations to Prof. Matt Hutchings for winning the [https://microbiologysociety.org/news/society-news/professor-matt-hutchings-wins-the-2019-microbiology-outreach-prize.html 2019 Outreach Prize]!

==Outreach Events Calendar==

Are you presenting your actinobacteria research at a science festival, [https://pintofscience.co.uk/ Pint of Science], [https://twitter.com/soapboxscience?lang=en Soapbox Science], or other outreach event? Let us know so that we can add you to our [[Outreach Events Calendar]]!

=Student pages=
If you would like to use ActinoBase for a wiki creation/editing assignment as part of a course or workshop, please [[Admin contact page|contact]] us.

=Other resources=

==Blogs==
*[https://microbiologysociety.org/news-press/microbe-post.html Microbe Post]
*[https://schaechter.asmblog.org/ Small Things Considered]

==Podcasts==
*[https://soundcloud.com/microbiosoc Microbe Talk]
*[https://www.asm.org/Podcasts/TWiM This Week in Microbiology]
*[https://www.asm.org/Podcasts/BacterioFiles BacterioFiles]
*[https://www.asm.org/Podcasts/microTalk microTalk]
*[https://www.asm.org/Podcasts/MTM Meet the Microbiologist]
*[http://naturalprodcast.com/ Natural Prodcast]

==Microbial Art==
The range of colored pigments produced by different actinobacteria, coupled with their tendency for non-lateral growth, make them suitable for creating biological art. Creating and observing biological art can be used as a vehicle to engage people with diverse backgrounds and interests in both concepts and techniques related to chemistry and biology.[https://doi.org/10.1371/journal.pbio.1000510 1]

“Agar art” has been shown to be an effective method for increasing confidence in students being introduced to microbiology.[https://doi.org/10.1093/femsle/fnx245 2] Similarly, as long as proper sterile conditions are available, creating art using ''Streptomyces'' has been an engaging activity for introducing high school students to microbiology and working with elementary school populations. BioArt employing actinobacteria can therefore be used to introduce both younger students and artists to science, including those from traditionally marginalized identities in STEM.[https://doi.org/10.1371/journal.pbio.3000061 3]

The following strains are streaked, using sterile technique, on R5 media in order to “draw” with their pigments. The strains can also be streaked on a modified, less expensive media using food-grade agar and/or chicken broth. Pigments appear after 3-7 days of growth.[https://doi.org/10.1371/journal.pbio.1000510 1] All ''Streptomyces'' strains are classified as Biosafety Level 1 (BSL-1) organisms, and are of minimal hazard to humans.[https://doi.org/10.1002/9780471729259.mc10e01s18 4]
* ''Streptomyces coelicolor'' (Blue, Red under acidic conditions)
* ''Streptomyces violaceoruber'' (Purple, Pink under acidic conditions)
* ''Streptomyces roseofulvus'' (Yellow)

The colored pigments can also be extracted, dried, and resuspended in acrylic to produce bio-based paint.

Using standard 100 mm petri dishes allows for smaller-scale activities, which is often preferable when introducing proper bacterial streaking technique so that participants can create multiple pieces of art. However, using larger plates allows experienced artists to create much more detailed and intricate drawings.

[[File:BioArt.png|450px]][https://doi.org/10.1371/journal.pbio.3000061 3] [[File:BioArtElvis.PNG|310px]][https://doi.org/10.1371/journal.pbio.1000510 1]

The characteristic colored pigments produced by actinobacterial strains enable concurrent learning opportunities about molecular color and natural products. While leading or introducing the activity, participants may be interested to learn that biosynthesized molecules are responsible for the drawing’s vibrant color and that these molecules can have antibiotic and anticancer properties.

References:

1. Charkoudian, L.K., Fitzgerald, J.T., Khosla, C., Champlin, A., 2010. In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8, e1000510. https://doi.org/10.1371/journal.pbio.1000510

2. Adkins, S.J., Rock, R.K., Morris, J.J., 2018. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS Microbiology Letters 365. https://doi.org/10.1093/femsle/fnx245

3. Lopes, L.E., Waldis, S.J., Terrell, S.M., Lindgren, K.A., Charkoudian, L.K., 2018. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 16, e3000061. https://doi.org/10.1371/journal.pbio.3000061

4. Shepherd, M.D., Kharel, M.K., Bosserman, M.A., Rohr, J., 2010. Laboratory Maintenance of Streptomyces Species. Current Protocols in Microbiology 18. https://doi.org/10.1002/9780471729259.mc10e01s18

Teaching and learning

2021-11-18T12:38:53Z

Nelly:

=Teaching and Learning=

This is the hub for #ActinoBase teaching and learning resources: educational content, outreach, and more! We welcome contributions from the community, so please [[Admin contact page|contact]] us with any suggestions or if you would like to contribute content to these pages.

==Practical protocols (undergrad labs)==

==Bioinformatics ==
*A practical lesson on [https://carpentries-incubator.github.io/metagenomics-workshop/ Metagenomics].
*R, python, Linux, Git and other lessons at [https://software-carpentry.org/lessons/ Software Carpentries].

==Undergraduate student projects==

*[https://seaphages.org/ SEA-PHAGES], an HHMI undergraduate course featuring the discovery and isolation of actinobacteriophages
*[https://www.strath.ac.uk/viprojects/drugdiscovery/ the Strathclyde VIP Drug Discovery Project], using hyperspectral imaging to screen for novel antibiotic producers

==Spotlight: teaching antibiotics & AMR==

Are you looking for videos to use in your courses, inspiration for classroom or workshop activities, or other resources to help you with your teaching? Please check out our collection of [[Teaching and Learning Resources: Antibiotics and AMR]].

==Other teaching and learning resources==
*[https://microbiologyonline.org/teachers Microbiology Society resources for teachers]
*[https://microbiologyonline.org/students Microbiology Society resources for students]
*[https://www.asmscience.org/VisualLibrary the American Society for Microbiology's resource library]
*[https://www.asmscience.org/content/journal/jmbe Journal of Microbiology and Biology Education]
*[https://schaechter.asmblog.org/schaechter/teachers-corner-1/ Small Things Considered: Teacher's Corner]
*[http://www.actino.jp/index-e.html]

=Outreach=
[https://www.uea.ac.uk/research/explore-uea-research/antibiotic-hunters Antibiotic Hunters]: Huge congratulations to Prof. Matt Hutchings for winning the [https://microbiologysociety.org/news/society-news/professor-matt-hutchings-wins-the-2019-microbiology-outreach-prize.html 2019 Outreach Prize]!

==Outreach Events Calendar==

Are you presenting your actinobacteria research at a science festival, [https://pintofscience.co.uk/ Pint of Science], [https://twitter.com/soapboxscience?lang=en Soapbox Science], or other outreach event? Let us know so that we can add you to our [[Outreach Events Calendar]]!

=Student pages=
If you would like to use ActinoBase for a wiki creation/editing assignment as part of a course or workshop, please [[Admin contact page|contact]] us.

=Other resources=

==Blogs==
*[https://microbiologysociety.org/news-press/microbe-post.html Microbe Post]
*[https://schaechter.asmblog.org/ Small Things Considered]

==Podcasts==
*[https://soundcloud.com/microbiosoc Microbe Talk]
*[https://www.asm.org/Podcasts/TWiM This Week in Microbiology]
*[https://www.asm.org/Podcasts/BacterioFiles BacterioFiles]
*[https://www.asm.org/Podcasts/microTalk microTalk]
*[https://www.asm.org/Podcasts/MTM Meet the Microbiologist]
*[http://naturalprodcast.com/ Natural Prodcast]

==Microbial Art==
The range of colored pigments produced by different actinobacteria, coupled with their tendency for non-lateral growth, make them suitable for creating biological art. Creating and observing biological art can be used as a vehicle to engage people with diverse backgrounds and interests in both concepts and techniques related to chemistry and biology.[https://doi.org/10.1371/journal.pbio.1000510 1]

“Agar art” has been shown to be an effective method for increasing confidence in students being introduced to microbiology.[https://doi.org/10.1093/femsle/fnx245 2] Similarly, as long as proper sterile conditions are available, creating art using ''Streptomyces'' has been an engaging activity for introducing high school students to microbiology and working with elementary school populations. BioArt employing actinobacteria can therefore be used to introduce both younger students and artists to science, including those from traditionally marginalized identities in STEM.[https://doi.org/10.1371/journal.pbio.3000061 3]

The following strains are streaked, using sterile technique, on R5 media in order to “draw” with their pigments. The strains can also be streaked on a modified, less expensive media using food-grade agar and/or chicken broth. Pigments appear after 3-7 days of growth.[https://doi.org/10.1371/journal.pbio.1000510 1] All ''Streptomyces'' strains are classified as Biosafety Level 1 (BSL-1) organisms, and are of minimal hazard to humans.[https://doi.org/10.1002/9780471729259.mc10e01s18 4]
* ''Streptomyces coelicolor'' (Blue, Red under acidic conditions)
* ''Streptomyces violaceoruber'' (Purple, Pink under acidic conditions)
* ''Streptomyces roseofulvus'' (Yellow)

The colored pigments can also be extracted, dried, and resuspended in acrylic to produce bio-based paint.

Using standard 100 mm petri dishes allows for smaller-scale activities, which is often preferable when introducing proper bacterial streaking technique so that participants can create multiple pieces of art. However, using larger plates allows experienced artists to create much more detailed and intricate drawings.

[[File:BioArt.png|450px]][https://doi.org/10.1371/journal.pbio.3000061 3] [[File:BioArtElvis.PNG|310px]][https://doi.org/10.1371/journal.pbio.1000510 1]

The characteristic colored pigments produced by actinobacterial strains enable concurrent learning opportunities about molecular color and natural products. While leading or introducing the activity, participants may be interested to learn that biosynthesized molecules are responsible for the drawing’s vibrant color and that these molecules can have antibiotic and anticancer properties.

References:

1. Charkoudian, L.K., Fitzgerald, J.T., Khosla, C., Champlin, A., 2010. In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8, e1000510. https://doi.org/10.1371/journal.pbio.1000510

2. Adkins, S.J., Rock, R.K., Morris, J.J., 2018. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS Microbiology Letters 365. https://doi.org/10.1093/femsle/fnx245

3. Lopes, L.E., Waldis, S.J., Terrell, S.M., Lindgren, K.A., Charkoudian, L.K., 2018. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 16, e3000061. https://doi.org/10.1371/journal.pbio.3000061

4. Shepherd, M.D., Kharel, M.K., Bosserman, M.A., Rohr, J., 2010. Laboratory Maintenance of Streptomyces Species. Current Protocols in Microbiology 18. https://doi.org/10.1002/9780471729259.mc10e01s18

Teaching and learning

2021-11-18T12:38:28Z

Nelly: /* Bioinformatics */

=Teaching and Learning=

This is the hub for #ActinoBase teaching and learning resources: educational content, outreach, and more! We welcome contributions from the community, so please [[Admin contact page|contact]] us with any suggestions or if you would like to contribute content to these pages.

==Practical protocols (undergrad labs)==
==Bioinformatics ==

- A practical lesson on [https://carpentries-incubator.github.io/metagenomics-workshop/ Metagenomics].
- R, python, Linux, Git and other lessons at [https://software-carpentry.org/lessons/ Software Carpentries].

==Undergraduate student projects==

*[https://seaphages.org/ SEA-PHAGES], an HHMI undergraduate course featuring the discovery and isolation of actinobacteriophages
*[https://www.strath.ac.uk/viprojects/drugdiscovery/ the Strathclyde VIP Drug Discovery Project], using hyperspectral imaging to screen for novel antibiotic producers

==Spotlight: teaching antibiotics & AMR==

Are you looking for videos to use in your courses, inspiration for classroom or workshop activities, or other resources to help you with your teaching? Please check out our collection of [[Teaching and Learning Resources: Antibiotics and AMR]].

==Other teaching and learning resources==
*[https://microbiologyonline.org/teachers Microbiology Society resources for teachers]
*[https://microbiologyonline.org/students Microbiology Society resources for students]
*[https://www.asmscience.org/VisualLibrary the American Society for Microbiology's resource library]
*[https://www.asmscience.org/content/journal/jmbe Journal of Microbiology and Biology Education]
*[https://schaechter.asmblog.org/schaechter/teachers-corner-1/ Small Things Considered: Teacher's Corner]
*[http://www.actino.jp/index-e.html]

=Outreach=
[https://www.uea.ac.uk/research/explore-uea-research/antibiotic-hunters Antibiotic Hunters]: Huge congratulations to Prof. Matt Hutchings for winning the [https://microbiologysociety.org/news/society-news/professor-matt-hutchings-wins-the-2019-microbiology-outreach-prize.html 2019 Outreach Prize]!

==Outreach Events Calendar==

Are you presenting your actinobacteria research at a science festival, [https://pintofscience.co.uk/ Pint of Science], [https://twitter.com/soapboxscience?lang=en Soapbox Science], or other outreach event? Let us know so that we can add you to our [[Outreach Events Calendar]]!

=Student pages=
If you would like to use ActinoBase for a wiki creation/editing assignment as part of a course or workshop, please [[Admin contact page|contact]] us.

=Other resources=

==Blogs==
*[https://microbiologysociety.org/news-press/microbe-post.html Microbe Post]
*[https://schaechter.asmblog.org/ Small Things Considered]

==Podcasts==
*[https://soundcloud.com/microbiosoc Microbe Talk]
*[https://www.asm.org/Podcasts/TWiM This Week in Microbiology]
*[https://www.asm.org/Podcasts/BacterioFiles BacterioFiles]
*[https://www.asm.org/Podcasts/microTalk microTalk]
*[https://www.asm.org/Podcasts/MTM Meet the Microbiologist]
*[http://naturalprodcast.com/ Natural Prodcast]

==Microbial Art==
The range of colored pigments produced by different actinobacteria, coupled with their tendency for non-lateral growth, make them suitable for creating biological art. Creating and observing biological art can be used as a vehicle to engage people with diverse backgrounds and interests in both concepts and techniques related to chemistry and biology.[https://doi.org/10.1371/journal.pbio.1000510 1]

“Agar art” has been shown to be an effective method for increasing confidence in students being introduced to microbiology.[https://doi.org/10.1093/femsle/fnx245 2] Similarly, as long as proper sterile conditions are available, creating art using ''Streptomyces'' has been an engaging activity for introducing high school students to microbiology and working with elementary school populations. BioArt employing actinobacteria can therefore be used to introduce both younger students and artists to science, including those from traditionally marginalized identities in STEM.[https://doi.org/10.1371/journal.pbio.3000061 3]

The following strains are streaked, using sterile technique, on R5 media in order to “draw” with their pigments. The strains can also be streaked on a modified, less expensive media using food-grade agar and/or chicken broth. Pigments appear after 3-7 days of growth.[https://doi.org/10.1371/journal.pbio.1000510 1] All ''Streptomyces'' strains are classified as Biosafety Level 1 (BSL-1) organisms, and are of minimal hazard to humans.[https://doi.org/10.1002/9780471729259.mc10e01s18 4]
* ''Streptomyces coelicolor'' (Blue, Red under acidic conditions)
* ''Streptomyces violaceoruber'' (Purple, Pink under acidic conditions)
* ''Streptomyces roseofulvus'' (Yellow)

The colored pigments can also be extracted, dried, and resuspended in acrylic to produce bio-based paint.

Using standard 100 mm petri dishes allows for smaller-scale activities, which is often preferable when introducing proper bacterial streaking technique so that participants can create multiple pieces of art. However, using larger plates allows experienced artists to create much more detailed and intricate drawings.

[[File:BioArt.png|450px]][https://doi.org/10.1371/journal.pbio.3000061 3] [[File:BioArtElvis.PNG|310px]][https://doi.org/10.1371/journal.pbio.1000510 1]

The characteristic colored pigments produced by actinobacterial strains enable concurrent learning opportunities about molecular color and natural products. While leading or introducing the activity, participants may be interested to learn that biosynthesized molecules are responsible for the drawing’s vibrant color and that these molecules can have antibiotic and anticancer properties.

References:

1. Charkoudian, L.K., Fitzgerald, J.T., Khosla, C., Champlin, A., 2010. In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8, e1000510. https://doi.org/10.1371/journal.pbio.1000510

2. Adkins, S.J., Rock, R.K., Morris, J.J., 2018. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS Microbiology Letters 365. https://doi.org/10.1093/femsle/fnx245

3. Lopes, L.E., Waldis, S.J., Terrell, S.M., Lindgren, K.A., Charkoudian, L.K., 2018. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 16, e3000061. https://doi.org/10.1371/journal.pbio.3000061

4. Shepherd, M.D., Kharel, M.K., Bosserman, M.A., Rohr, J., 2010. Laboratory Maintenance of Streptomyces Species. Current Protocols in Microbiology 18. https://doi.org/10.1002/9780471729259.mc10e01s18

Teaching and learning

2021-11-18T12:37:59Z

Nelly: /* Bioinformatics */

=Teaching and Learning=

This is the hub for #ActinoBase teaching and learning resources: educational content, outreach, and more! We welcome contributions from the community, so please [[Admin contact page|contact]] us with any suggestions or if you would like to contribute content to these pages.

==Practical protocols (undergrad labs)==
==Bioinformatics ==

A practical lesson on [https://carpentries-incubator.github.io/metagenomics-workshop/ Metagenomics]
R, python, Linux, Git and other lessons at [https://software-carpentry.org/lessons/ Software Carpentries]

==Undergraduate student projects==

*[https://seaphages.org/ SEA-PHAGES], an HHMI undergraduate course featuring the discovery and isolation of actinobacteriophages
*[https://www.strath.ac.uk/viprojects/drugdiscovery/ the Strathclyde VIP Drug Discovery Project], using hyperspectral imaging to screen for novel antibiotic producers

==Spotlight: teaching antibiotics & AMR==

Are you looking for videos to use in your courses, inspiration for classroom or workshop activities, or other resources to help you with your teaching? Please check out our collection of [[Teaching and Learning Resources: Antibiotics and AMR]].

==Other teaching and learning resources==
*[https://microbiologyonline.org/teachers Microbiology Society resources for teachers]
*[https://microbiologyonline.org/students Microbiology Society resources for students]
*[https://www.asmscience.org/VisualLibrary the American Society for Microbiology's resource library]
*[https://www.asmscience.org/content/journal/jmbe Journal of Microbiology and Biology Education]
*[https://schaechter.asmblog.org/schaechter/teachers-corner-1/ Small Things Considered: Teacher's Corner]
*[http://www.actino.jp/index-e.html]

=Outreach=
[https://www.uea.ac.uk/research/explore-uea-research/antibiotic-hunters Antibiotic Hunters]: Huge congratulations to Prof. Matt Hutchings for winning the [https://microbiologysociety.org/news/society-news/professor-matt-hutchings-wins-the-2019-microbiology-outreach-prize.html 2019 Outreach Prize]!

==Outreach Events Calendar==

Are you presenting your actinobacteria research at a science festival, [https://pintofscience.co.uk/ Pint of Science], [https://twitter.com/soapboxscience?lang=en Soapbox Science], or other outreach event? Let us know so that we can add you to our [[Outreach Events Calendar]]!

=Student pages=
If you would like to use ActinoBase for a wiki creation/editing assignment as part of a course or workshop, please [[Admin contact page|contact]] us.

=Other resources=

==Blogs==
*[https://microbiologysociety.org/news-press/microbe-post.html Microbe Post]
*[https://schaechter.asmblog.org/ Small Things Considered]

==Podcasts==
*[https://soundcloud.com/microbiosoc Microbe Talk]
*[https://www.asm.org/Podcasts/TWiM This Week in Microbiology]
*[https://www.asm.org/Podcasts/BacterioFiles BacterioFiles]
*[https://www.asm.org/Podcasts/microTalk microTalk]
*[https://www.asm.org/Podcasts/MTM Meet the Microbiologist]
*[http://naturalprodcast.com/ Natural Prodcast]

==Microbial Art==
The range of colored pigments produced by different actinobacteria, coupled with their tendency for non-lateral growth, make them suitable for creating biological art. Creating and observing biological art can be used as a vehicle to engage people with diverse backgrounds and interests in both concepts and techniques related to chemistry and biology.[https://doi.org/10.1371/journal.pbio.1000510 1]

“Agar art” has been shown to be an effective method for increasing confidence in students being introduced to microbiology.[https://doi.org/10.1093/femsle/fnx245 2] Similarly, as long as proper sterile conditions are available, creating art using ''Streptomyces'' has been an engaging activity for introducing high school students to microbiology and working with elementary school populations. BioArt employing actinobacteria can therefore be used to introduce both younger students and artists to science, including those from traditionally marginalized identities in STEM.[https://doi.org/10.1371/journal.pbio.3000061 3]

The following strains are streaked, using sterile technique, on R5 media in order to “draw” with their pigments. The strains can also be streaked on a modified, less expensive media using food-grade agar and/or chicken broth. Pigments appear after 3-7 days of growth.[https://doi.org/10.1371/journal.pbio.1000510 1] All ''Streptomyces'' strains are classified as Biosafety Level 1 (BSL-1) organisms, and are of minimal hazard to humans.[https://doi.org/10.1002/9780471729259.mc10e01s18 4]
* ''Streptomyces coelicolor'' (Blue, Red under acidic conditions)
* ''Streptomyces violaceoruber'' (Purple, Pink under acidic conditions)
* ''Streptomyces roseofulvus'' (Yellow)

The colored pigments can also be extracted, dried, and resuspended in acrylic to produce bio-based paint.

Using standard 100 mm petri dishes allows for smaller-scale activities, which is often preferable when introducing proper bacterial streaking technique so that participants can create multiple pieces of art. However, using larger plates allows experienced artists to create much more detailed and intricate drawings.

[[File:BioArt.png|450px]][https://doi.org/10.1371/journal.pbio.3000061 3] [[File:BioArtElvis.PNG|310px]][https://doi.org/10.1371/journal.pbio.1000510 1]

The characteristic colored pigments produced by actinobacterial strains enable concurrent learning opportunities about molecular color and natural products. While leading or introducing the activity, participants may be interested to learn that biosynthesized molecules are responsible for the drawing’s vibrant color and that these molecules can have antibiotic and anticancer properties.

References:

1. Charkoudian, L.K., Fitzgerald, J.T., Khosla, C., Champlin, A., 2010. In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8, e1000510. https://doi.org/10.1371/journal.pbio.1000510

2. Adkins, S.J., Rock, R.K., Morris, J.J., 2018. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS Microbiology Letters 365. https://doi.org/10.1093/femsle/fnx245

3. Lopes, L.E., Waldis, S.J., Terrell, S.M., Lindgren, K.A., Charkoudian, L.K., 2018. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 16, e3000061. https://doi.org/10.1371/journal.pbio.3000061

4. Shepherd, M.D., Kharel, M.K., Bosserman, M.A., Rohr, J., 2010. Laboratory Maintenance of Streptomyces Species. Current Protocols in Microbiology 18. https://doi.org/10.1002/9780471729259.mc10e01s18

Teaching and learning

2021-11-18T12:35:44Z

Nelly:

=Teaching and Learning=

This is the hub for #ActinoBase teaching and learning resources: educational content, outreach, and more! We welcome contributions from the community, so please [[Admin contact page|contact]] us with any suggestions or if you would like to contribute content to these pages.

==Practical protocols (undergrad labs)==
==Bioinformatics ==

==Undergraduate student projects==

*[https://seaphages.org/ SEA-PHAGES], an HHMI undergraduate course featuring the discovery and isolation of actinobacteriophages
*[https://www.strath.ac.uk/viprojects/drugdiscovery/ the Strathclyde VIP Drug Discovery Project], using hyperspectral imaging to screen for novel antibiotic producers

==Spotlight: teaching antibiotics & AMR==

Are you looking for videos to use in your courses, inspiration for classroom or workshop activities, or other resources to help you with your teaching? Please check out our collection of [[Teaching and Learning Resources: Antibiotics and AMR]].

==Other teaching and learning resources==
*[https://microbiologyonline.org/teachers Microbiology Society resources for teachers]
*[https://microbiologyonline.org/students Microbiology Society resources for students]
*[https://www.asmscience.org/VisualLibrary the American Society for Microbiology's resource library]
*[https://www.asmscience.org/content/journal/jmbe Journal of Microbiology and Biology Education]
*[https://schaechter.asmblog.org/schaechter/teachers-corner-1/ Small Things Considered: Teacher's Corner]
*[http://www.actino.jp/index-e.html]

=Outreach=
[https://www.uea.ac.uk/research/explore-uea-research/antibiotic-hunters Antibiotic Hunters]: Huge congratulations to Prof. Matt Hutchings for winning the [https://microbiologysociety.org/news/society-news/professor-matt-hutchings-wins-the-2019-microbiology-outreach-prize.html 2019 Outreach Prize]!

==Outreach Events Calendar==

Are you presenting your actinobacteria research at a science festival, [https://pintofscience.co.uk/ Pint of Science], [https://twitter.com/soapboxscience?lang=en Soapbox Science], or other outreach event? Let us know so that we can add you to our [[Outreach Events Calendar]]!

=Student pages=
If you would like to use ActinoBase for a wiki creation/editing assignment as part of a course or workshop, please [[Admin contact page|contact]] us.

=Other resources=

==Blogs==
*[https://microbiologysociety.org/news-press/microbe-post.html Microbe Post]
*[https://schaechter.asmblog.org/ Small Things Considered]

==Podcasts==
*[https://soundcloud.com/microbiosoc Microbe Talk]
*[https://www.asm.org/Podcasts/TWiM This Week in Microbiology]
*[https://www.asm.org/Podcasts/BacterioFiles BacterioFiles]
*[https://www.asm.org/Podcasts/microTalk microTalk]
*[https://www.asm.org/Podcasts/MTM Meet the Microbiologist]
*[http://naturalprodcast.com/ Natural Prodcast]

==Microbial Art==
The range of colored pigments produced by different actinobacteria, coupled with their tendency for non-lateral growth, make them suitable for creating biological art. Creating and observing biological art can be used as a vehicle to engage people with diverse backgrounds and interests in both concepts and techniques related to chemistry and biology.[https://doi.org/10.1371/journal.pbio.1000510 1]

“Agar art” has been shown to be an effective method for increasing confidence in students being introduced to microbiology.[https://doi.org/10.1093/femsle/fnx245 2] Similarly, as long as proper sterile conditions are available, creating art using ''Streptomyces'' has been an engaging activity for introducing high school students to microbiology and working with elementary school populations. BioArt employing actinobacteria can therefore be used to introduce both younger students and artists to science, including those from traditionally marginalized identities in STEM.[https://doi.org/10.1371/journal.pbio.3000061 3]

The following strains are streaked, using sterile technique, on R5 media in order to “draw” with their pigments. The strains can also be streaked on a modified, less expensive media using food-grade agar and/or chicken broth. Pigments appear after 3-7 days of growth.[https://doi.org/10.1371/journal.pbio.1000510 1] All ''Streptomyces'' strains are classified as Biosafety Level 1 (BSL-1) organisms, and are of minimal hazard to humans.[https://doi.org/10.1002/9780471729259.mc10e01s18 4]
* ''Streptomyces coelicolor'' (Blue, Red under acidic conditions)
* ''Streptomyces violaceoruber'' (Purple, Pink under acidic conditions)
* ''Streptomyces roseofulvus'' (Yellow)

The colored pigments can also be extracted, dried, and resuspended in acrylic to produce bio-based paint.

Using standard 100 mm petri dishes allows for smaller-scale activities, which is often preferable when introducing proper bacterial streaking technique so that participants can create multiple pieces of art. However, using larger plates allows experienced artists to create much more detailed and intricate drawings.

[[File:BioArt.png|450px]][https://doi.org/10.1371/journal.pbio.3000061 3] [[File:BioArtElvis.PNG|310px]][https://doi.org/10.1371/journal.pbio.1000510 1]

The characteristic colored pigments produced by actinobacterial strains enable concurrent learning opportunities about molecular color and natural products. While leading or introducing the activity, participants may be interested to learn that biosynthesized molecules are responsible for the drawing’s vibrant color and that these molecules can have antibiotic and anticancer properties.

References:

1. Charkoudian, L.K., Fitzgerald, J.T., Khosla, C., Champlin, A., 2010. In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8, e1000510. https://doi.org/10.1371/journal.pbio.1000510

2. Adkins, S.J., Rock, R.K., Morris, J.J., 2018. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS Microbiology Letters 365. https://doi.org/10.1093/femsle/fnx245

3. Lopes, L.E., Waldis, S.J., Terrell, S.M., Lindgren, K.A., Charkoudian, L.K., 2018. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 16, e3000061. https://doi.org/10.1371/journal.pbio.3000061

4. Shepherd, M.D., Kharel, M.K., Bosserman, M.A., Rohr, J., 2010. Laboratory Maintenance of Streptomyces Species. Current Protocols in Microbiology 18. https://doi.org/10.1002/9780471729259.mc10e01s18

Sequence databases

2021-11-18T12:21:07Z

Nelly:

[https://www.embl.de EMBL]

[https://www.ncbi.nlm.nih.gov NCBI]

[https://img.jgi.doe.gov/ IMG/M]

[https://genome.jgi.doe.gov/portal/ JGI Genome Portal]

[https://antismash-db.secondarymetabolites.org/ AntiSMASH DB] 1
*A database with an overview of the available biosynthetic gene cluster predictions. It is possible to browse the database by phylogeny or secondary metabolite type.

[https://mibig.secondarymetabolites.org/ MIBiG] 2
*Minimal information for Biosynthetic gene clusters. The Minimum Information about a Biosynthetic Gene cluster (MIBiG) contains annotations and metadata on experimentally validated biosynthetic gene clusters and their molecular products.

[https://bigfam.bioinformatics.nl/home BIG FAM] 3
*BiG-FAM is a database of thousands of gene cluster families that captures the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). BiG-SLiCE is the algorithm behind BiG-FAM.

#Kai Blin; Simon Shaw; Satria A. Kautsar; Marnix H. Medema; Tilmann Weber. (2020) The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes Nucleic Acids Research , gkaa978; doi: 10.1093/nar/gkaa978
#Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema, (2020) MIBiG 2.0: a repository for biosynthetic gene clusters of known function, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D454–D458, https://doi.org/10.1093/nar/gkz882
#Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, (2021) Nucleic Acids Research, Volume 49, Issue D1, Pages D490–D497, https://doi.org/10.1093/nar/gkaa812

Sequence databases

2021-11-18T12:20:46Z

Nelly:

Sequence databases

2021-11-18T12:20:17Z

Nelly:

[https://www.embl.de EMBL]

[https://www.ncbi.nlm.nih.gov NCBI]

[https://img.jgi.doe.gov/ IMG/M]

[https://genome.jgi.doe.gov/portal/ JGI Genome Portal]

[https://antismash-db.secondarymetabolites.org/ AntiSMASH DB] 1
A database with an overview of the available biosynthetic gene cluster predictions. It is possible to browse the database by phylogeny or secondary metabolite type.

[https://mibig.secondarymetabolites.org/ MIBiG] 2

*Minimal information for Biosynthetic gene clusters
The Minimum Information about a Biosynthetic Gene cluster (MIBiG) contains annotations and metadata on experimentally validated biosynthetic gene clusters and their molecular products.

[https://bigfam.bioinformatics.nl/home BIG FAM] 3
BiG-FAM is a database of thousands of gene cluster families that captures the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). BiG-SLiCE is the algorithm behind BiG-FAM.

#Kai Blin; Simon Shaw; Satria A. Kautsar; Marnix H. Medema; Tilmann Weber. (2020) The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes Nucleic Acids Research , gkaa978; doi: 10.1093/nar/gkaa978
#Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema, (2020) MIBiG 2.0: a repository for biosynthetic gene clusters of known function, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D454–D458, https://doi.org/10.1093/nar/gkz882
#Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, (2021) Nucleic Acids Research, Volume 49, Issue D1, Pages D490–D497, https://doi.org/10.1093/nar/gkaa812

Sequence databases

2021-11-18T00:18:16Z

Nelly:

[https://www.embl.de EMBL]

[https://www.ncbi.nlm.nih.gov NCBI]

[https://img.jgi.doe.gov/ IMG/M]

[https://genome.jgi.doe.gov/portal/ JGI Genome Portal]

[https://antismash-db.secondarymetabolites.org/ AntiSMASH DB] 1
It is possible to browse the database by phylogeny or secondary metabolite type, giving an exploratory overview of the avaliable biosynthetic gene cluster predictions

[https://mibig.secondarymetabolites.org/ MIBiG] 2

*Minimal information for Biosynthetic gene clusters
The Minimum Information about a Biosynthetic Gene cluster (MIBiG) specification provides a robust community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. MIBiG is a Genomic Standards Consortium project that builds on the Minimum Information about any Sequence (MIxS) framework.

[https://bigfam.bioinformatics.nl/home BIG FAM] 3
BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs).

#Kai Blin; Simon Shaw; Satria A. Kautsar; Marnix H. Medema; Tilmann Weber. (2020) The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes Nucleic Acids Research , gkaa978; doi: 10.1093/nar/gkaa978
#Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema, (2020) MIBiG 2.0: a repository for biosynthetic gene clusters of known function, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D454–D458, https://doi.org/10.1093/nar/gkz882
#Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, (2021) Nucleic Acids Research, Volume 49, Issue D1, Pages D490–D497, https://doi.org/10.1093/nar/gkaa812

Sequence databases

2021-11-18T00:01:06Z

Nelly:

Sequence databases

2021-11-17T23:58:37Z

Nelly:

Sequence databases

2021-11-17T23:56:47Z

Nelly:

Genome mining tools

2021-11-17T23:52:13Z

Nelly:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterized biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

[https://antismash.secondarymetabolites.org/#!/start antiSMASH]:1 (antibiotics and Secondary Metabolite Analysis Shell)
*Identification and annotation of secondary metabolite gene clusters
*[https://twitter.com/antiSMASH_dev Twitter]

[http://grid.adapsyn.com/prism/#!/prism PRISM]:2 (PRediction Informatics for Secondary Metabolism)
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

[http://bagel4.molgenrug.nl/ BAGEL]:3
* Identification of gene clusters for bacteriocins and RiPPs

[https://omictools.com/clusean-tool CLUSEAN]:4
*Annotation and analysis of secondary metabolite gene clusters

[https://github.com/petercim/ClusterFinder ClusterFinder]:5
*Identification of secondary metabolite gene clusters

[https://arts3.ziemertlab.com/ ARTS]:6 (Antibiotic Resistant Target Seeker)
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

[https://sourceforge.net/projects/secmetdb/ 2metDB]:7
*Genome mining for polyketides and nonribosomal peptides

[http://pks.kaist.ac.kr/pkminer/ PKMiner]:8
*Genome mining for type II polyketide synthases

[http://www.nii.ac.in/sbspks2.html SBSPKS]:9
*Sequence analysis of polyketide synthases

[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php RiPPMINER]:10
*Genome mining and deciphering chemical structures of RiPPs

[http://www.ripprodeo.org/manual.html RODEO]:11 (Rapid ORF Description and Evaluation Online)
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

[https://github.com/streptomyces/ripper RiPPER]:12
*Identification of RiPP precursor peptides and biosynthetic gene clusters
*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

[https://bigscape-corason.secondarymetabolites.org/BiG-SCAPE]:13
*Identification of gene cluster families through a collection of genomes. This software classifies antiSMASH outputs into cluster families. Also on this paper, software CORASON searches any gene cluster in a set of genomes.

[https://github.com/nselem/EvoMining/wiki EvoMining]:14
*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

[https://github.com/medema-group/bigslice BiG SLiCE ]:15
*Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.

# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 1; 39 doi: 10.1093/nar/gkr466
# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. et al, Nucleic Acids Research, doi: 10.1093/nar/gkx320
# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 2;46 doi: org/10.1093/nar/gky383.
# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) Cell, 158:412-21 doi: 10.1016/j.cell.2014.06.034
# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Research, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiology, 8;12:169. doi: 10.1186/1471-2180-12-169.
# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. Nucleic Acids Research, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research, 3;45 doi: 10.1093/nar/gkx408.
# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nature Chemical Biology, 13(5):470-478 doi: 10.1038/nchembio.2319.
# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Research, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microbial Genomics https://doi.org/10.1099/mgen.0.000260
# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, GigaScience, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154

Genome mining tools

2021-11-17T23:51:36Z

Nelly:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterized biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

[https://antismash.secondarymetabolites.org/#!/start antiSMASH]:1 (antibiotics and Secondary Metabolite Analysis Shell)
*Identification and annotation of secondary metabolite gene clusters
*[https://twitter.com/antiSMASH_dev Twitter]

[http://grid.adapsyn.com/prism/#!/prism PRISM]:2 (PRediction Informatics for Secondary Metabolism)
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

[http://bagel4.molgenrug.nl/ BAGEL]:3
* Identification of gene clusters for bacteriocins and RiPPs

[https://omictools.com/clusean-tool CLUSEAN]:4
*Annotation and analysis of secondary metabolite gene clusters

[https://github.com/petercim/ClusterFinder ClusterFinder]:5
*Identification of secondary metabolite gene clusters

[https://arts3.ziemertlab.com/ ARTS]:6 (Antibiotic Resistant Target Seeker)
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

[https://sourceforge.net/projects/secmetdb/ 2metDB]:7
*Genome mining for polyketides and nonribosomal peptides

[http://pks.kaist.ac.kr/pkminer/ PKMiner]:8
*Genome mining for type II polyketide synthases

[http://www.nii.ac.in/sbspks2.html SBSPKS]:9
*Sequence analysis of polyketide synthases

[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php RiPPMINER]:10
*Genome mining and deciphering chemical structures of RiPPs

[http://www.ripprodeo.org/manual.html RODEO]:11 (Rapid ORF Description and Evaluation Online)
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

[https://github.com/streptomyces/ripper RiPPER]:12
*Identification of RiPP precursor peptides and biosynthetic gene clusters
*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

[https://bigscape-corason.secondarymetabolites.org/BiG-SCAPE]:13
*Identification of gene cluster families through a collection of genomes. This software classifies antiSMASH outputs into cluster families. Also on this paper, software CORASON searches any gene cluster in a set of genomes.

[https://github.com/nselem/EvoMining/wiki EvoMining]:14
*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

[https://github.com/medema-group/bigslice BiG SLiCE]:15
*Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.

# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 1; 39 doi: 10.1093/nar/gkr466
# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. et al, Nucleic Acids Research, doi: 10.1093/nar/gkx320
# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 2;46 doi: org/10.1093/nar/gky383.
# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) Cell, 158:412-21 doi: 10.1016/j.cell.2014.06.034
# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Research, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiology, 8;12:169. doi: 10.1186/1471-2180-12-169.
# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. Nucleic Acids Research, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research, 3;45 doi: 10.1093/nar/gkx408.
# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nature Chemical Biology, 13(5):470-478 doi: 10.1038/nchembio.2319.
# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Research, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microbial Genomics https://doi.org/10.1099/mgen.0.000260
# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, GigaScience, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154

Genome mining tools

2021-11-17T23:50:43Z

Nelly:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterized biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

[https://antismash.secondarymetabolites.org/#!/start antiSMASH]:1 (antibiotics and Secondary Metabolite Analysis Shell)
*Identification and annotation of secondary metabolite gene clusters
*[https://twitter.com/antiSMASH_dev Twitter]

[http://grid.adapsyn.com/prism/#!/prism PRISM]:2 (PRediction Informatics for Secondary Metabolism)
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

[http://bagel4.molgenrug.nl/ BAGEL]:3
* Identification of gene clusters for bacteriocins and RiPPs

[https://omictools.com/clusean-tool CLUSEAN]:4
*Annotation and analysis of secondary metabolite gene clusters

[https://github.com/petercim/ClusterFinder ClusterFinder]:5
*Identification of secondary metabolite gene clusters

[https://arts3.ziemertlab.com/ ARTS]:6 (Antibiotic Resistant Target Seeker)
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

[https://sourceforge.net/projects/secmetdb/ 2metDB]:7
*Genome mining for polyketides and nonribosomal peptides

[http://pks.kaist.ac.kr/pkminer/ PKMiner]:8
*Genome mining for type II polyketide synthases

[http://www.nii.ac.in/sbspks2.html SBSPKS]:9
*Sequence analysis of polyketide synthases

[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php RiPPMINER]:10
*Genome mining and deciphering chemical structures of RiPPs

[http://www.ripprodeo.org/manual.html RODEO]:11 (Rapid ORF Description and Evaluation Online)
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

[https://github.com/streptomyces/ripper RiPPER]:12
*Identification of RiPP precursor peptides and biosynthetic gene clusters
*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

[https://bigscape-corason.secondarymetabolites.org/BiG-SCAPE]:13
*Identification of gene cluster families through a collection of genomes. This software classifies antiSMASH outputs into cluster families. Also on this paper, software CORASON searches any gene cluster in a set of genomes.

[https://github.com/nselem/EvoMining/wiki EvoMining]:14
*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

[https://github.com/medema-group/bigslice BiG SLiCE]
* Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.

# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 1; 39 doi: 10.1093/nar/gkr466
# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. et al, Nucleic Acids Research, doi: 10.1093/nar/gkx320
# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 2;46 doi: org/10.1093/nar/gky383.
# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) Cell, 158:412-21 doi: 10.1016/j.cell.2014.06.034
# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Research, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiology, 8;12:169. doi: 10.1186/1471-2180-12-169.
# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. Nucleic Acids Research, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research, 3;45 doi: 10.1093/nar/gkx408.
# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nature Chemical Biology, 13(5):470-478 doi: 10.1038/nchembio.2319.
# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Research, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microbial Genomics https://doi.org/10.1099/mgen.0.000260
e
# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, GigaScience, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154

16S rRNA metaprofiling

2021-11-17T23:40:29Z

Nelly:

[https://greengenes.secondgenome.com Green Genes] 16S rRNA gene database

[https://www.arb-silva.de/ SILVA] 16S, 18S, SSU & LSU rRNA gene database

[http://qiime.org QIIME™] or [https://www.mothur.org Mothur] or [http://benjjneb.github.io/dada2/ dada2] for analyzing 16S rRNA gene sequences.

Genome mining tools

2021-11-17T20:17:53Z

Nelly: addin big scpae reference and CORASON description

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterized biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

[https://antismash.secondarymetabolites.org/#!/start antiSMASH]:1 (antibiotics and Secondary Metabolite Analysis Shell)
*Identification and annotation of secondary metabolite gene clusters
*[https://twitter.com/antiSMASH_dev Twitter]

[http://grid.adapsyn.com/prism/#!/prism PRISM]:2 (PRediction Informatics for Secondary Metabolism)
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

[http://bagel4.molgenrug.nl/ BAGEL]:3
* Identification of gene clusters for bacteriocins and RiPPs

[https://omictools.com/clusean-tool CLUSEAN]:4
*Annotation and analysis of secondary metabolite gene clusters

[https://github.com/petercim/ClusterFinder ClusterFinder]:5
*Identification of secondary metabolite gene clusters

[https://arts3.ziemertlab.com/ ARTS]:6 (Antibiotic Resistant Target Seeker)
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

[https://sourceforge.net/projects/secmetdb/ 2metDB]:7
*Genome mining for polyketides and nonribosomal peptides

[http://pks.kaist.ac.kr/pkminer/ PKMiner]:8
*Genome mining for type II polyketide synthases

[http://www.nii.ac.in/sbspks2.html SBSPKS]:9
*Sequence analysis of polyketide synthases

[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php RiPPMINER]:10
*Genome mining and deciphering chemical structures of RiPPs

[http://www.ripprodeo.org/manual.html RODEO]:11 (Rapid ORF Description and Evaluation Online)
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

[https://github.com/streptomyces/ripper RiPPER]:12
*Identification of RiPP precursor peptides and biosynthetic gene clusters
*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

[https://bigscape-corason.secondarymetabolites.org/BiG-SCAPE]:13
*Identification of gene cluster families through a collection of genomes. This software classifies antiSMASH outputs into cluster families. Also on this paper, software CORASON searches any gene cluster in a set of genomes.

[https://github.com/nselem/EvoMining/wiki EvoMining]:14
*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 1; 39 doi: 10.1093/nar/gkr466
# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. et al, Nucleic Acids Research, doi: 10.1093/nar/gkx320
# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 2;46 doi: org/10.1093/nar/gky383.
# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) Cell, 158:412-21 doi: 10.1016/j.cell.2014.06.034
# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Research, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiology, 8;12:169. doi: 10.1186/1471-2180-12-169.
# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. Nucleic Acids Research, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research, 3;45 doi: 10.1093/nar/gkx408.
# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nature Chemical Biology, 13(5):470-478 doi: 10.1038/nchembio.2319.
# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Research, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microbial Genomics https://doi.org/10.1099/mgen.0.000260

Genome mining tools

2021-11-17T19:45:11Z

Nelly:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterized biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

[https://antismash.secondarymetabolites.org/#!/start antiSMASH]:1 (antibiotics and Secondary Metabolite Analysis Shell)
*Identification and annotation of secondary metabolite gene clusters
*[https://twitter.com/antiSMASH_dev Twitter]

[http://grid.adapsyn.com/prism/#!/prism PRISM]:2 (PRediction Informatics for Secondary Metabolism)
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

[http://bagel4.molgenrug.nl/ BAGEL]:3
* Identification of gene clusters for bacteriocins and RiPPs

[https://omictools.com/clusean-tool CLUSEAN]:4
*Annotation and analysis of secondary metabolite gene clusters

[https://github.com/petercim/ClusterFinder ClusterFinder]:5
*Identification of secondary metabolite gene clusters

[https://arts3.ziemertlab.com/ ARTS]:6 (Antibiotic Resistant Target Seeker)
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

[https://sourceforge.net/projects/secmetdb/ 2metDB]:7
*Genome mining for polyketides and nonribosomal peptides

[http://pks.kaist.ac.kr/pkminer/ PKMiner]:8
*Genome mining for type II polyketide synthases

[http://www.nii.ac.in/sbspks2.html SBSPKS]:9
*Sequence analysis of polyketide synthases

[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php RiPPMINER]:10
*Genome mining and deciphering chemical structures of RiPPs

[http://www.ripprodeo.org/manual.html RODEO]:11 (Rapid ORF Description and Evaluation Online)
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

[https://github.com/streptomyces/ripper RiPPER]:12
*Identification of RiPP precursor peptides and biosynthetic gene clusters
*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

[https://omictools.com/big-scape-tool BiG-SCAPE]:13
*Identification of gene clusters families

[https://github.com/nselem/EvoMining/wiki EvoMining]:14
*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 1; 39 doi: 10.1093/nar/gkr466
# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. et al, Nucleic Acids Research, doi: 10.1093/nar/gkx320
# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 2;46 doi: org/10.1093/nar/gky383.
# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) Cell, 158:412-21 doi: 10.1016/j.cell.2014.06.034
# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Research, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiology, 8;12:169. doi: 10.1186/1471-2180-12-169.
# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. Nucleic Acids Research, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research, 3;45 doi: 10.1093/nar/gkx408.
# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nature Chemical Biology, 13(5):470-478 doi: 10.1038/nchembio.2319.
# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Research, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microbial Genomics 2019 . https://doi.org/10.1099/mgen.0.000260

Sequence databases

2021-11-17T19:29:36Z

Nelly: reference to databases

Sequence databases

2021-11-12T18:32:14Z

Nelly: Adding databases

[https://www.embl.de EMBL]

[https://www.ncbi.nlm.nih.gov NCBI]

[https://img.jgi.doe.gov/ IMG/M]

[https://genome.jgi.doe.gov/portal/ JGI Genome Portal]

[https://antismash-db.secondarymetabolites.org/ AntiSMASH DB]

[https://mibig.secondarymetabolites.org/ MIBiG]

[https://bigfam.bioinformatics.nl/home BIG FAM]