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Open Access Highly Accessed Software

The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Scott A Givan12*, Christopher M Sullivan12 and James C Carrington12

Author Affiliations

1 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA

2 Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA

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BMC Bioinformatics 2007, 8:479  doi:10.1186/1471-2105-8-479

Published: 18 December 2007

Abstract

Background

Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist.

Results

We present the Personal Sequence Database (PSD), a suite of tools to create and maintain small- to medium-sized web-accessible sequence databases. All interactions with PSD tools occur via the internet with a web browser. Users may define sequence groups within their database that can be maintained privately or published to the web for public use. A sequence group can be downloaded, browsed, searched by keyword or searched for sequence similarities using BLAST. Publishing a sequence group extends these capabilities to colleagues and collaborators. In addition to being able to manage their own sequence databases, users can enroll sequences in BLASTAgent, a BLAST hit tracking system, to monitor NCBI databases for new entries displaying a specified level of nucleotide or amino acid similarity.

Conclusion

The PSD offers a valuable set of resources unavailable elsewhere. In addition to managing sequence data and BLAST search results, it facilitates data sharing with colleagues, collaborators and public users. The PSD is hosted by the authors and is available at http://bioinfo.cgrb.oregonstate.edu/psd/ webcite.