Let me create an rRNA sequence database having a web front-end for that lab Sometimes in. It appears common in biology to wish to look a lot of sequences using alignment calculations for example BLAST and HMMER, and so i wondered if there's any existing php/python/rails projects that permit easy development of a normal sequence database having a website search form?

UPDATE: GMOD is the kind of server I had been searching for. I had been also recommended to check out BioMart too which looks to possess a similar functionality.

something rather less barebones is http://gmod.org/ - the easiest installation should provide you with a blast form &lifier a "sequence browser" interface. Have no idea if there is a hmmer form yet...

(scales pretty much - from the simple sqlite to some real database)

Alternatively, you might want to consider the universe server. http://primary.g2.bx.psu.edu/
It's first goal is making complex genomic queries simple for non-computational people however i have no idea if it features a blast as they are

cheers, yannick


UPDATE - Inspired simply with this publish, we're creating a simple local blast server being an easy-to-deploy option to wwwblast. Work happening at http://world wide web.sequenceserver.com. A demo server allows you BLAST ant genomes.

This is overkill most likely but.... ncbi provides extensive software available. Link.

Particularly, this.

There is a simple CGI front-finish distributed using the NCBI BLAST package too. You are able to download it using their FTP site, that is here:

ftp://ftp.ncbi.nih.gov/

It isn't either from the language you're speaking about, but there's BioPERL, the industry assortment of functions particularly designed for DNA and RNA along with other acidity and protein base 'programming'

Search for it in CPAN.org

I'd highly recommend getting in touch with the bioinformatics community. The most crucial factor would be to design the database and choose its purpose. You mention DNA within the title but rRNA within the text - they are different things. Whether it's merely a typo, fine - but when you do not comprehend the difference then talk to people locally.

Since I am active in the community you may want to contact the MyExperiment community (http://en.wikipedia.org/wiki/MyExperiment) and mention my title if you want to. You will find plenty of friendly people and help.

UPDATE I have just observed you're from Manchester and that is the hub of MyExperiment so it truly is the apparent starting point!

Concerning GMOD: I'm relatively certain GMOD is complete overkill for the application. GMOD isn't a server, it's an accumulation of tools, the database schema (CHADO) being one of these, and Chado isn't for somebody who mostly may have sequences and ids. BioMart isn't a server either, it is a tool that enables p-normalization of model databases, to have the ability to run whole-genome queries fast enough. Among the BioMart clients (MartView) may come as an internet interface. You certainly don't wish to use Biomart right now however i can explain that at length by email. I've the sense that you simply rather require a web-based BLAST client to obtain began first.