I’d like to create an rRNA sequence database with a web front end for the lab I work in. It seems common in biology to want to search a large number of sequences using alignment algorithms such as BLAST and HMMER, so I wondered if there is any existing php/python/rails projects that allow easy creation of a generic sequence database with a website search form?
UPDATE: GMOD is the type of server I was looking for. I was also suggested to look at BioMart too which looks to have a similar functionality.
something a little less barebones is http://gmod.org/ – the simplest installation should give you a blast form & a “sequence browser” interface.
Don’t know if theres a hmmer form yet…
(scales pretty well – from a simple sqlite to a real database)
Alternatively, you may want to look into the galaxy server. http://main.g2.bx.psu.edu/
It’s first aim is making complex genomic queries easy for non-computational people but I dont know if it has a blast out of the box
cheers,
yannick
UPDATE – Inspired in part by this post, we are developing a simple local blast server as an easy-to-deploy alternative to wwwblast. Work in progress at http://www.sequenceserver.com. A demo server lets you BLAST ant genomes.