BLAST Filter and GraphicAlign: Rule-based formation and analysis of sets of related DNA and protein sequences

John B. Spalding, Peter J. Lammers

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)W26-W32
JournalNucleic acids research
Volume32
Issue numberWEB SERVER ISS.
DOIs
StatePublished - Jul 1 2004
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics

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