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Effective detection of remote homologues by searching in sequence dataset of a protein domain fold
Author(s) -
Sandhya S,
Kishore S,
Sowdhamini R,
Srinivasan N
Publication year - 2003
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(03)00929-3
Subject(s) - sequence (biology) , computational biology , fold (higher order function) , computer science , conserved sequence , sequence database , biology , base sequence , genetics , gene , programming language
Profile matching methods are commonly used in searches in protein sequence databases to detect evolutionary relationships. We describe here a sensitive protocol, which detects remote similarities by searching in a specialized database of sequences belonging to a fold. We have assessed this protocol by exploring the relationships we detect among sequences known to belong to specific folds. We find that searches within sequences adopting a fold are more effective in detecting remote similarities and evolutionary connections than searches in a database of all sequences. We also discuss the implications of using this strategy to link sequence and structure space.