An Algorithm to Classify Amino Acid Sequences into Protein Groups of Bothrops jararacussu Venomous Gland
Abstract:An algorithm for automatic clustering of database protein sequences from Bothrops jararacussu venomous gland, according to sequence similarities of their domains, is described. The program was written in C and Perl languages. This algorithm compares a domain with each ORF protein sequence in the database. Each nucleotide FASTA sequence generates six ORFs. As a result, the user has a list containing all sequences found in a specific domain and a display of the sequence, domain and number of hits. The algorithm lists only the sequences that present a minimum similarity of 30 hits and the best alignment. This limit was considered appropriate. The algorithm is available in the Internet (www.compbionet.org.br/cgi-domains/homesnake) and it can quickly and accurately organizes large database into classes.
Document Type: Review Article
Affiliations: Unidade de Biotecnologia, Universidade de Ribeirao Preto, UNAERP, 14096-380, Ribeirao Preto - SP, Brazil.
Publication date: 2005-05-01
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