1. SeqDepot: streamlined database of biological sequences and precomputed features
- Author
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Igor B. Zhulin and Luke E. Ulrich
- Subjects
Statistics and Probability ,Computer science ,JavaScript ,computer.software_genre ,Biochemistry ,Databases, Genetic ,Humans ,Web application ,Molecular Biology ,computer.programming_language ,Internet ,HTML5 ,Database ,business.industry ,Computational Biology ,Sequence Analysis, DNA ,Python (programming language) ,Applications Notes ,Computer Science Applications ,Computational Mathematics ,Task (computing) ,Computational Theory and Mathematics ,Scripting language ,Perl ,business ,computer ,Software - Abstract
Summary: 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/. REST access via http://seqdepot.net/api/v1. Database files and scripts may be downloaded from http://seqdepot.net/download. Contact: ulrich.luke+sci@gmail.com
- Published
- 2013
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