Open AccessBLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences
Author(s) -
Judson W. Spalding,
Peter J. Lammers
Publication year - 2004
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkh459
Subject(s) - redundancy (engineering) , filter (signal processing) , biology , computer science , sequence (biology) , set (abstract data type) , sequence alignment , sequence analysis , multiple sequence alignment , sequence database , data mining , computational biology , genetics , dna , peptide sequence , gene , computer vision , programming language , operating system
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.
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