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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.
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GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).
Of these, the most important are the equivalent DNA databases European Molecular Biology Laboratory (EMBL), GenBank and DNA Databank of Japan (DDBJ), and the protein databases Swiss-Prot and TrEMBL. The commonly used BLAST and FASTA algorithms are described in detail and alternative approaches mentioned briefly.
GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects.
Many species- and taxa-specific genome databases have made use of this standard, open-source set of database tools. The RGD, TAIR, Gramene, FlyBase, MGI, SGD, and WormBase databases are just a few. Sometimes, these tools are the main foundation of a database; in other cases, they supplement existing databases.
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.
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