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Open Access Software

SNAD: sequence name annotation-based designer

Igor A Sidorov1, Denis A Reshetov2 and Alexander E Gorbalenya12*

Author Affiliations

1 Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, E4-P, 2300 RC Leiden, Netherlands

2 Faculty of Bioengineering and Bioinformatics, Moscow State University, 119899 Moscow, Russia

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BMC Bioinformatics 2009, 10:251  doi:10.1186/1471-2105-10-251

Published: 14 August 2009

Abstract

Background

A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions.

Results

Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology.

Conclusion

A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.