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Nucleic Acids Research 2006 34(Web Server issue):W591-W595; doi:10.1093/nar/gkl337
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

FeatureScan: revealing property-dependent similarity of nucleotide sequences

Igor V. Deyneko1,2,*, Björn Bredohl1,4, Daniel Wesely1,4, Yulia M. Kalybaeva1, Alexander E. Kel3, Helmut Blöcker1,* and Gerhard Kauer1,4

1 Department of Genome Analysis, GBF (German Research Centre for Biotechnology) D-38124 Braunschweig, Germany 2 Institute of Cytology and Genetics SB RAS, Novosibirsk Russia 3 BIOBASE GmbH, D-38300 Wolfenbüttel Germany 4 University of Applied Sciences, D-26723 Emden Germany

*To whom correspondence should be addressed. Tel: +49 531 6181 224; Fax: +49 531 6181 292; Email: ide{at}gbf.de

Received February 14, 2006. Revised March 1, 2006. Accepted April 17, 2006.

FeatureScan is a software package aiming to reveal novel types of DNA sequence similarity by comparing physico-chemical properties. Thirty-eight different parameters of DNA double strands such as charge, melting enthalpy, conformational parameters and the like are provided. As input FeatureScan requires two sequences, a pattern sequence and a target sequence, search conditions are set by selecting a specific DNA parameter and a threshold value. Search results are displayed in FASTA format and directly linked to external genome databases/browsers (ENSEMBL, NCBI, UCSC). An Internet version of FeatureScan is accessible at http://genome.gbf.de/featurescan/. As part of the HOBIT initiative (http://hobit.sourceforge.net/) FeatureScan is also accessible as a web service at its above home page. Currently, several preloaded genomes are provided at this Internet website (Homo sapiens, Mus musculus, Rattus norvegicus and four strains of Escherichia coli) as target sequences. Standalone executables of FeatureScan are available on request.

*Correspondence may also be addressed to Helmut Blöcker. Tel: +49 531 6181 220; Fax: +49 531 6181 292; Email: bloecker{at}gbf.de


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