Links

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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

Expasy translate tool

MEME: for identification of DNA binding sites in ChIP-seq data

NEB Restriction enzyme cutter

Tables of Streptomyces coelicolor reciprocal BLASTP hits

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:

antiSMASH:1 (antibiotics and Secondary Metabolite Analysis Shell)

  • Identification and annotation of secondary metabolite gene clusters
  • Twitter

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

ClusterFinder:5

  • 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

BiG-SCAPE

EvoMining

References

  1. 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
  2. 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
  3. 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.
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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

EMBL

NCBI

IMG/M

JGI Genome Portal


Genomes

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.

Additional Streptomyces resources including the StrepDB genome database