Doing a little survey/snooping around. Trying to compile a list of available online tools for annotating microbial genomes and metagenomes. And I am also trying to get comments on what people think of the various tools. There are some obvious candidates to think about
- IMG and IMG/M
- RAST and MG-RAST
- IGS annotation engine (which seems to no longer be a web server but an email the sequence to someone server).
But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.
- Jonathan Eisen @phylogenomics
- Researching blog post on free/online microbial genome/metagenome annotation services – looking for examples beyond IMG & RAST
- Mick Watson @BioMickWatson
- @phylogenomics some microbial annotation pipelines mentioned in our review here bib.oxfordjournals.org/content/early/…
- Ewan Birney @ewanbirney
- @phylogenomics Check out @EBImetagenomics ebi.ac.uk/metagenomics/: ORFs, Interproscan, submissions and more.
- Mick Watson @BioMickWatson
- @ewanbirney @phylogenomics @EBImetagenomics needs illumina support, and support of assemblies
And from Google Plus where I asked “Researching blog post on free/online microbial genome/metagenome annotation services – looking for examples beyond IMG & RAST “:
- Mary Mangan – Oh, I know some:
- Manatee: http://www.jcvi.org/cms/research/projects/annotation-service/
- GATU: http://athena.bioc.uvic.ca/virology-ca-tools/gatu/
- Apollo: http://gmod.org/wiki/Apollo
- And also from Mary
- Here’s a question on that at BioStar:
- EDIT: Another question suggests Artemis:
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Jonathan Eisen's Lab 
From an email — someone pointed to the NCBI annotation pipeline
http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html
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Also see
http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter9.html
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And from Google +
Peter Cook: Also there is BASys (Bacterial Annotation System), http://basys.ca
Rob Edwards: see http://edwards.sdsu.edu/rtmg/
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*Discrete cough* Its Peter Cock actually, not Cook – but that happens a lot 😉
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oops
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Thanks for gathering all this information into one place. Can we add some links to standards of genome annotation? In some bacteria for one example the tefA gene is annotated as a second copy of the fusA gene. The fusA encodes EF-G, the ribosomal translocase, while tefA encoded the ribosomal back-transloacase. They are quite similar in sequence, stucture and function so it is understandable that some annotators would confuse the two.
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