S4: structure-based sequence alignments of SCOP superfamilies | Zendy

James A Casbon | Zendy

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S4: structure-based sequence alignments of SCOP superfamilies

Author(s) -

James A Casbon

Publication year - 2004

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki043

Subject(s) - compendium , biology , structural alignment , sequence alignment , sequence (biology) , computational biology , sequence database , pairwise comparison , alignment free sequence analysis , multiple sequence alignment , bioinformatics , computer science , genetics , peptide sequence , artificial intelligence , gene , archaeology , history

S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included. The alignments are constructed using pairwise structural alignments to generate residue equivalences that are then integrated into multiple alignments using sequence alignment tools. We describe the database and give examples showing how the automatically generated S4 alignments compare favourably to hand-crafted alignments. Available at: http://compbio.mds.qmw.ac.uk/S4.html.

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