J Newitt at 15:49, 10 October 2019

2019-10-10T15:49:25Z

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


			==Genomes==

			[[File:Actinobase-icons-trans_Background.png\|150px\|Genomes\|link=Genomes]]

			[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]==

J Newitt at 15:45, 10 October 2019

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	[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</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		# 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

J Newitt: Created page with "=Useful Links= ==Bioinformatics== ===16S rRNA metaprofiling=== [https://greengenes.secondgenome.com Green Genes] 16S rRNA gene database [https://www.arb-silva.de/ SILVA]..."

2019-10-10T15:44:15Z

Created page with "=Useful Links= ==Bioinformatics== ===16S rRNA metaprofiling=== [https://greengenes.secondgenome.com Green Genes] 16S rRNA gene database [https://www.arb-silva.de/ SILVA]..."

New page

=Useful Links=

==Bioinformatics==

===16S rRNA metaprofiling===

[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]

===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 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

[https://omictools.com/big-scape-tool BiG-SCAPE]

[https://github.com/nselem/EvoMining/wiki EvoMining]

# 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

PDB: https://www.rcsb.org/
*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===

[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]

Links master page - Revision history

J Newitt at 15:49, 10 October 2019

J Newitt at 15:45, 10 October 2019

J Newitt: Created page with "=Useful Links= ==Bioinformatics== ===16S rRNA metaprofiling=== [https://greengenes.secondgenome.com Green Genes] 16S rRNA gene database [https://www.arb-silva.de/ SILVA]..."