Sunday, March 11, 2012

Wanted - opinions/details on online systems for annotation of genomes and metagenomes

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
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
  • Ewan Birney ‏ @ewanbirney 
  • 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 ":




-
Labels: ,

5 comments:

  1. Jonathan Eisen3/14/2012 11:46 AM

    From an email --- someone pointed to the NCBI annotation pipeline

    http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html

    ReplyDelete
  2. Jonathan Eisen3/15/2012 10:28 AM

    Also see

    http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter9.html

    ReplyDelete
  3. Jonathan Eisen3/15/2012 10:29 AM

    And from Google +

    Peter Cook: Also there is BASys (Bacterial Annotation System), http://basys.ca

    Rob Edwards: see http://edwards.sdsu.edu/rtmg/

    ReplyDelete
  4. Peter Cock3/20/2012 3:43 PM

    *Discrete cough* Its Peter Cock actually, not Cook - but that happens a lot ;)

    ReplyDelete
  5. Anonymous5/18/2013 7:36 AM

    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.

    ReplyDelete

Subscribe to: Post Comments (Atom)

Most recent post

Talk on Sequencing and Microbes ...

I recently gave a talk where I combined what are normally two distinct topics - the Evolution of DNA Sequencing, and the use of Sequencing t...