02541nam a2200277 a 450000100080000000500110000800800410001910000160006024501000007626001760017630000110035250000760036352015710043965000230201065000130203365300220204665300320206865300210210065300250212170000220214670000210216870000240218970000150221370000190222870000160224710089672020-01-17       2005    bl uuuu     u00u1 u    #d1 aHIGA, R. H.  aBuilding multiple sequence alignments with a flavour of HSSP alignments.h[electronic resource]  aIn: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacionalc2005  ap. 28.  aX-meeting 2005. Presented Posters. Na publicação: Paula Regina Kuser.  aHSSP is a well-know database of 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 databank. It is also used by STING and JavaProtein Dossier to calculate and present relative entropy as a measurement of a 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 have to have a new method for building alignments having a flavour of HSSP alignments (myMSAr). This work presents this new method and its corresponding databank (SH2Qs - database of Sequences Homologue to the Query [Structure-having] Sequence). Our main interest on making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless if it has a corresponding structure deposited in the PDB databank. In this work, we compare the measurement of residue conservation provided by corresponding alignments produced by the HSSP and SH2Qs. As a case study, we also present two biologically relevant examples, the former one highlighting the equivalence of analysis of a degree of residue conservation by using HSSP or SH2Qs alignments, and the later one presenting the degree of residue conservation for a structure modeled in a computer and, as a consequence, which does not have alignment reported by HSSP.  aSequence alignment  aProteina  aEntropia relativa  aMultiple sequence alignment  aRelative entropy  aResidue conservation1 aCRUZ, S. A. B. da1 aFALCAO, P. R. K.1 aYAMAGISHI, M. E. B.1 aFILETO, R.1 aMANCINI, A. L.1 aNESHICH, G.