Large-scale comparison of protein sequence alignment algorithms with structure alignments

Sequence alignment programs such as BLAST and PSI‐BLAST are used routinely in pairwise, profile‐based, or intermediate‐sequence‐search (ISS) methods to detect remote homologies for the purposes of fold assignment and comparative modeling. Yet, the sequence alignment quality of these methods at low s...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2000-07, Vol.40 (1), p.6-22
Main Authors: Sauder, J. Michael, Arthur, Jonathan W., Dunbrack Jr, Roland L.
Format: Article
Language:English
Subjects:
Algorithms
alignment benchmark
Databases, Factual
homology modeling
intermediate sequence
Protein Structure, Secondary
Proteins - chemistry
PSI-BLAST
SCOP
Sequence Alignment - methods
Sequence Homology, Amino Acid
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Summary:Sequence alignment programs such as BLAST and PSI‐BLAST are used routinely in pairwise, profile‐based, or intermediate‐sequence‐search (ISS) methods to detect remote homologies for the purposes of fold assignment and comparative modeling. Yet, the sequence alignment quality of these methods at low sequence identity is not known. We have used the CE structure alignment program (Shindyalov and Bourne, Prot Eng 1998;11:739) to derive sequence alignments for all superfamily and family‐level related proteins in the SCOP domain database. CE aligns structures and their sequences based on distances within each protein, rather than on interprotein distances. We compared BLAST, PSI‐BLAST, CLUSTALW, and ISS alignments with the CE structural alignments. We found that global alignments with CLUSTALW were very poor at low sequence identity (
ISSN:0887-3585
1097-0134
DOI:10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7