title: 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.
authors.affiliation: Unidade de Biotecnologia, Universidade de Ribeirao Preto, UNAERP, SP, Brazil.
authors.forename: Silvana
authors.initials: S
authors.lastname: Giuliatti
authors.forename: Milton
authors.initials: M
authors.lastname: Faria
authors.forename: Fernando
authors.initials: F
authors.lastname: Camargo
authors.forename: Luiz Paulo
authors.initials: LP
authors.lastname: Camargo
authors.forename: Suzelei C
authors.initials: SC
authors.lastname: Franca
authors.forename: Andreimar M
authors.initials: AM
authors.lastname: Soares
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation; D017837:Bothrops; D019295:Computational Biology / Q000379:methods*; D003435:Crotalid Venoms / Q000737:chemistry*; D030562:Databases, Protein; D005088:Exocrine Glands; D008969:Molecular Sequence Data
chemical_list: D003435:Crotalid Venoms