SeqDepot: streamlined database of biological sequences and precomputed features

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


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 RESTaccess via Database files and scripts maybe downloaded from

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology*
  • Databases, Genetic*
  • Humans
  • Internet
  • Sequence Analysis, DNA / methods*
  • Software*