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=Useful Links= | |||
==Bioinformatics== | |||
===16S rRNA metaprofiling=== | |||
[http://streptomyces.org.uk Additional <em>Streptomyces</em> resources including the StrepDB genome database] | [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] for analyzing 16S rRNA gene sequences. | |||
===Genome-based taxonomic analysis=== | |||
[https://tygs.dsmz.de/ TYGS] Type (Strain) Genome Server | |||
===DNA sequence analysis=== | |||
[https://www.ebi.ac.uk/Tools/msa/clustalo/ Clustal Omega sequence alignment] | |||
[https://web.expasy.org/translate/ Expasy translate tool] | |||
[http://meme-suite.org MEME: for identification of DNA binding sites in ChIP-seq data ] | |||
[http://nc2.neb.com/NEBcutter2/ NEB Restriction enzyme cutter] | |||
[http://streptomyces.org.uk/actinoblast/ Tables of Streptomyces coelicolor reciprocal BLASTP hits] | |||
[https://rfam.xfam.org// RNA family database] | |||
===Genome mining tools=== | |||
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 uncharacterised biosynthetic gene clusters (BGCs) for natural products. | |||
Some useful genome mining resources are listed below: | |||
[https://antismash.secondarymetabolites.org/#!/start <strong>antiSMASH</strong>]:<sup>1</sup> (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 <strong>PRISM</strong>]:<sup>2</sup> (PRediction Informatics for Secondary Metabolism) | |||
*Identification of nonribosomal peptides, type I and II polyketides and RiPPs | |||
[http://bagel4.molgenrug.nl/ <strong>BAGEL</strong>]:<sup>3</sup> | |||
* Identification of gene clusters for bacteriocins and RiPPs | |||
[https://omictools.com/clusean-tool <strong>CLUSEAN</strong>]:<sup>4</sup> | |||
*Annotation and analysis of secondary metabolite gene clusters | |||
[https://github.com/petercim/ClusterFinder <strong>ClusterFinder</strong>]:<sup>5</sup> | |||
*Identification of secondary metabolite gene clusters | |||
[https://arts3.ziemertlab.com/ <strong>ARTS</strong>]:<sup>6</sup> (Antibiotic Resistant Target Seeker) | |||
*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets | |||
[https://sourceforge.net/projects/secmetdb/ <strong>2metDB</strong>]:<sup>7</sup> | |||
*Genome mining for polyketides and nonribosomal peptides | |||
[http://pks.kaist.ac.kr/pkminer/ <strong>PKMiner</strong>]:<sup>8</sup> | |||
*Genome mining for type II polyketide synthases | |||
[http://www.nii.ac.in/sbspks2.html <strong>SBSPKS</strong>]:<sup>9</sup> | |||
*Sequence analysis of polyketide synthases | |||
[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php <strong>RiPPMINER</strong>]:<sup>10</sup> | |||
*Genome mining and deciphering chemical structures of RiPPs | |||
[http://www.ripprodeo.org/manual.html <strong>RODEO</strong>]:<sup>11</sup> (Rapid ORF Description and Evaluation Online) | |||
*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides | |||
[https://github.com/streptomyces/ripper <strong>RiPPER</strong>]:<sup>12</sup> | |||
*Identification of RiPP precursor peptides and biosynthetic gene clusters | |||
[https://omictools.com/big-scape-tool <strong>BiG-SCAPE</strong>] | |||
[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</strong>] | |||
====References==== | |||
# 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. <em>Nucleic Acids Research</em>, 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. <em>et al, Nucleic Acids Research</em>, 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 web server to thoroughly mine RiPPs and bacteriocins. <em>Nucleic Acids Research</em>, 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. <em>Journal of Biotechnology</em>, 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) <em>Cell</em>, 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. <em>Nucleic Acids Research</em>, 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. <em>Methods in Enzymology</em>, 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. <em>BMC Microbiology</em>, 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. <em>Nucleic Acids Research</em>, 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. <em>Nucleic Acids Research</em>, 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. <em>Nature Chemical Biology</em>, 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. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192 | |||
===Protein & peptide analysis=== | |||
Useful resources for analysing protein and peptide features, structures and families: | |||
<strong>STRING</strong>: https://string-db.org/ | |||
*Protein-Protein Interaction Networks | |||
<strong>pFam</strong>: https://pfam.xfam.org/ | |||
*Database of protein families | |||
<strong>Phobius</strong>: http://phobius.cbr.su.se/ | |||
*Combined transmembrane topology and signal peptide predictor | |||
<strong>SignalP</strong>: http://www.cbs.dtu.dk/services/SignalP/ | |||
*Signal peptide predictor | |||
<strong>PDB</strong>: https://www.rcsb.org/ | |||
*Protein data bank | |||
<strong>Phyre2</strong>: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index | |||
*Protein fold recognition | |||
<strong>ExPASy</strong>: https://expasy.org/proteomics | |||
*Collection of proteomics resources | |||
<strong>MEME suite</strong>: http://meme-suite.org/tools/meme | |||
*Motif-based sequence analysis | |||
===Sequence 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] | |||
==Genomes== | |||
[[File:Actinobase-icons-trans_Background.png|150px|Genomes|link=Genomes]] | |||
[https://detoxbase.org/projects/Microbiology/ActinoBase ActinoBase MORF Genome Browser ] | |||
[http://strepdb.streptomyces.org.uk/cgi-bin/dc3.pl?accession=AL645882&start=4291472&end=4302043&iorm=map&width=900 StrepDB]: the <em>Streptomyces</em> genome database curated by the [http://www.jic.ac.uk John Innes Centre], Norwich, UK. | |||
[http://avermitilis.ls.kitasato-u.ac.jp <em>Streptomyces avermitilis</em> genome project] | |||
[https://www.sanger.ac.uk/resources/downloads/bacteria/streptomyces-coelicolor.html <em>Streptomyces coelicolor</em> genome project] | |||
[https://www.sanger.ac.uk/resources/downloads/bacteria/streptomyces-scabies.html <em>Streptomyces scabies</em> genome project] | |||
==Suppliers== | |||
[https://www.biost.com BioS&T]: custom made genome libraries including bacterial two hybrid and ePAC clone libraries for capturing complete biosynthetic gene clusters. | |||
[http://www.mrdnalab.com Mr DNA]: for fast, cheap and reliable 16S, 18S & ITS rDNA amplicon sequencing for community profiling. | |||
[https://www.vertis-biotech.com/Home Vertis Biotech]: cappable RNA-sequencing for mapping transcript start sites and all other RNA-seq techniques. | |||
[https://www.dsmz.de DSMZ]: supplier of a broad variety of actinomycetes. | |||
==[http://streptomyces.org.uk Additional <em>Streptomyces</em> resources including the StrepDB genome database]== |
Latest revision as of 15:57, 20 February 2020
Useful Links
Bioinformatics
16S rRNA metaprofiling
Green Genes 16S rRNA gene database
SILVA 16S, 18S, SSU & LSU rRNA gene database
QIIME™ or Mothur for analyzing 16S rRNA gene sequences.
Genome-based taxonomic analysis
TYGS Type (Strain) Genome Server
DNA sequence analysis
Clustal Omega sequence alignment
MEME: for identification of DNA binding sites in ChIP-seq data
Tables of Streptomyces coelicolor reciprocal BLASTP hits
Genome mining tools
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 uncharacterised biosynthetic gene clusters (BGCs) for natural products.
Some useful genome mining resources are listed below:
antiSMASH:1 (antibiotics and Secondary Metabolite Analysis Shell)
- Identification and annotation of secondary metabolite gene clusters
PRISM:2 (PRediction Informatics for Secondary Metabolism)
- Identification of nonribosomal peptides, type I and II polyketides and RiPPs
BAGEL:3
- Identification of gene clusters for bacteriocins and RiPPs
CLUSEAN:4
- Annotation and analysis of secondary metabolite gene clusters
- Identification of secondary metabolite gene clusters
ARTS:6 (Antibiotic Resistant Target Seeker)
- Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets
2metDB:7
- Genome mining for polyketides and nonribosomal peptides
PKMiner:8
- Genome mining for type II polyketide synthases
SBSPKS:9
- Sequence analysis of polyketide synthases
RiPPMINER:10
- Genome mining and deciphering chemical structures of RiPPs
RODEO:11 (Rapid ORF Description and Evaluation Online)
- Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides
RiPPER:12
- Identification of RiPP precursor peptides and biosynthetic gene clusters
References
- 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 web server 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
Protein & peptide analysis
Useful resources for analysing protein and peptide features, structures and families:
STRING: https://string-db.org/
- Protein-Protein Interaction Networks
pFam: https://pfam.xfam.org/
- Database of protein families
Phobius: http://phobius.cbr.su.se/
- Combined transmembrane topology and signal peptide predictor
SignalP: http://www.cbs.dtu.dk/services/SignalP/
- Signal peptide predictor
- Protein data bank
Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
- Protein fold recognition
ExPASy: https://expasy.org/proteomics
- Collection of proteomics resources
MEME suite: http://meme-suite.org/tools/meme
- Motif-based sequence analysis
Sequence databases
Genomes
ActinoBase MORF Genome Browser
StrepDB: the Streptomyces genome database curated by the John Innes Centre, Norwich, UK.
Streptomyces avermitilis genome project
Streptomyces coelicolor genome project
Streptomyces scabies genome project
Suppliers
BioS&T: custom made genome libraries including bacterial two hybrid and ePAC clone libraries for capturing complete biosynthetic gene clusters.
Mr DNA: for fast, cheap and reliable 16S, 18S & ITS rDNA amplicon sequencing for community profiling.
Vertis Biotech: cappable RNA-sequencing for mapping transcript start sites and all other RNA-seq techniques.
DSMZ: supplier of a broad variety of actinomycetes.