Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regina Kuser, Michel Eduardo Beleza Yamagishi, Renato Fileto, Stanley Robson de Medeiros Oliveira, Ivan MazoniM, Edgard Henrique dos Santos, Goran Neshich, Adauto Luiz Mancini
Published: March 31, 2006
Genet. Mol. Res. 5 (1) : 127-137
Cite this Article:
R.Hiroshi Higa, S.Aparecido da Cruz, P.Regina Kuser, M.Eduardo Be Yamagishi, R. Fileto, S.Robson de Oliveira, I. Mazoni, E.Henrique d Santos, G. Neshich, A.Luiz Mancini (2006). Building multiple sequence alignments with a flavor of HSSP alignments. Genet. Mol. Res. 5(1): 127-137.
About the Authors
Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regina Kuser, Michel Eduardo Beleza Yamagishi, Renato Fileto, Stanley Robson de Medeiros Oliveira, Ivan MazoniM, Edgard Henrique dos Santos, Goran Neshich, Adauto Luiz Mancini
Corresponding author
G. Neshich
E-mail: neshich@cbi.cnptia.embrapa.br
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 JavaProtein 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 JavaProtein 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 flavor1 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.
Key words: Multiple sequence alignment, Residue conservation, MSA, HSSP, SH2QS, Relative entropy.