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Bioinformatics. 2014 Jan 15;30(2):295-7. doi: 10.1093/bioinformatics/btt658. Epub 2013 Nov 13.

SeqDepot: streamlined database of biological sequences and precomputed features.

Author information

1
Agile Genomics, LLC, Mount Pleasant, SC 29466, USA, Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Abstract

Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines.

AVAILABILITY:

Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.

PMID:
24234005
PMCID:
PMC3892692
DOI:
10.1093/bioinformatics/btt658
[Indexed for MEDLINE]
Free PMC Article

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