title: Building multiple sequence alignments with a flavor of HSSP alignments.
abstract: Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.
authors.affiliation: Centro Nacional de Pesquisa em Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil.
authors.forename: Roberto Hiroshi
authors.initials: RH
authors.lastname: Higa
authors.forename: Sergio Aparecido Braga da
authors.initials: SA
authors.lastname: Cruz
authors.forename: Paula Regina
authors.initials: PR
authors.lastname: Kuser
authors.forename: Michel Eduardo Beleza
authors.initials: ME
authors.lastname: Yamagishi
authors.forename: Renato
authors.initials: R
authors.lastname: Fileto
authors.forename: Stanley Robson de Medeiros
authors.initials: SR
authors.lastname: Oliveira
authors.forename: Ivan
authors.initials: I
authors.lastname: Mazoni
authors.forename: Edgard Henrique dos
authors.initials: EH
authors.lastname: Santos
authors.forename: Adauto Luiz
authors.initials: AL
authors.lastname: Mancini
authors.forename: Goran
authors.initials: G
authors.lastname: Neshich
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics*; D019277:Entropy; D006801:Humans; D008957:Models, Genetic; D017433:Protein Structure, Secondary / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*