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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
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SeqDepot: streamlined database of biological sequences and precomputed features.

Luke E Ulrich1, Igor B Zhulin

  • 1Agile 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.

Bioinformatics (Oxford, England)
|November 16, 2013
PubMed
Summary
This summary is machine-generated.

SeqDepot is a novel database that integrates sequence data with feature information. It simplifies access to over 28.5 million sequences and 300 million features via a flexible RESTful API.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Existing resources for sequence and feature data are numerous but often redundant.
  • Assembling integrated knowledge from these resources is a challenging and time-consuming task.

Purpose of the Study:

  • To develop a novel database, SeqDepot, for assimilating primary sequences with predicted feature data.
  • To provide a simple and accessible means for retrieving and utilizing this integrated information.

Main Methods:

  • Developed SeqDepot, a database integrating >28.5 million sequences and >300 million features.
  • Implemented a well-documented and flexible RESTful API for data access.
  • Created an HTML5/JavaScript web application and provided Perl/Python scripts for pipeline integration.

Main Results:

  • SeqDepot offers streamlined access to a large, integrated dataset of biological sequences and their features.
  • The RESTful API supports various data retrieval methods, including subsetting, bulk queries, and searching by identifiers.
  • The accompanying web application and scripts facilitate user interaction and integration into local workflows.

Conclusions:

  • SeqDepot addresses the redundancy and complexity of accessing sequence and feature data.
  • The database and its associated tools offer a simplified and efficient solution for researchers.
  • Facilitates easier integration of sequence and feature data into biological research pipelines.