[BioRuby] ruby BLAST server (web frontend)

[Yannick Wurm]

Dear list & CC-ed,

let me quote a discussion from a while back ( http://answerpot.com/showthread.php?1292835-rails+blast+server ):

> I'd like to set up a small server for people to run BLAST against some of my sequences & see the results. 
> GMOD obviously comes to mind, but it seems like overkill. 
> And perhaps there is an almost automagic way to do this with ruby on rails. Has anyone done this yet?


There was no good solution at the time. Anurag Priyam & I have since been working on something that fills this need. Ben Woodcroft has recently been contributing as well. Check:
https://github.com/yannickwurm/sequenceserver or http://www.sequenceserver.com

Some things remain to be improved. But globally the software works great. Thus we thought to share our progress on the list that initiated it. An excerpt of the README highlights some features:

Ease of use for biologists:
 * intuitive and helpful web interface: automatic sequence type detection that helps choose appropriate BLAST method and database types
 * links to easily download sequences of BLAST hits
 * support for advanced options.

Rapid deployment for bioinformatics administrators:
 * assisted formatting of BLAST databases (with sequence type detection)
 * automatic discovery of formatted BLAST databases during startup
 * uses ruby's internal web server (on any open port) or Apache
 * add custom hyperlinks from hits (to your genome browser or custom database).


We have been using this as the web frontend for our ant genome blast at http://www.antgenomes.org since a few months. 

Comments, suggestions... and contributions are most welcome!

Cheers,

Anurag & Ben & Yannick



-----------------------------
  Ant Genomes & Evolution 
 http://yannick.poulet.org
    skype://yannickwurm
-----------------------------