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Nucleic Acids Research 2004 32(Web Server Issue):W26-W32; doi:10.1093/nar/gkh459
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences

John B. Spalding1,* and Peter J. Lammers1,2

1 Molecular Biology Program and 2 Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA

* To whom correspondence should be addressed. Tel: +1 505 646 5031; Fax: +1 505 646 3371; Email: spalding{at}nmsu.edu

Received February 13, 2004; Revised and Accepted April 26, 2004

BLAST Filter and GraphAlign are web-based tools that offer novel methods for building and analyzing sets of related (i.e. similar) DNA and protein sequences. They can be used separately or together. BLAST Filter generates related sequence sets in an automated, objective and reproducible way based on an input query sequence. Sequences matched by BLAST are filtered through a set of 15 user-configurable rules based on full-length query/subject comparisons, high-scoring segment pair statistics and the level of redundancy in the sequence set. Such sets can be used for multiple alignments, profile hidden Markov models and other bioinformatics applications, including GraphAlign, which provides several novel methods for analyzing global query/subject alignments along with graphical representations of sequence similarities. These services are available at the following URLs: http://darwin.nmsu.edu/cgi-bin/blast_filter.cgi and http://darwin.nmsu.edu/cgi-bin/graph_align.cgi.

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 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.


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