Protein database searches for multiple alignments.
- 1 July 1990
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 87 (14) , 5509-5513
- https://doi.org/10.1073/pnas.87.14.5509
Abstract
Protein database searches frequently can reveal biologically significant sequence relationships useful in understanding structure and function. Weak but meaningful sequence patterns can be obscured, however, by other similarities due only to chance. By searching a database for multiple as opposed to pairwise alignments, distant relationships are much more easily distinguished from background noise. Recent statistical results permit the power of this approach to be analyzed. Given a typical query sequence, an algorithm described here permits the current protein database to be searched for three-sequence alignments in less than 4 min. Such searches have revealed a variety of subtle relationships that pairwise search methods would be unable to detect.Keywords
This publication has 20 references indexed in Scilit:
- Automatic generation of primary sequence patterns from sets of related protein sequences.Proceedings of the National Academy of Sciences, 1990
- The Immunoglobulin Superfamily—Domains for Cell Surface RecognitionAnnual Review of Immunology, 1988
- Detecting homology of distantly related proteins with consensus sequencesJournal of Molecular Biology, 1987
- Profile analysis: detection of distantly related proteins.Proceedings of the National Academy of Sciences, 1987
- Amino acid sequence of human plasma alpha 1B-glycoprotein: homology to the immunoglobulin supergene family.Proceedings of the National Academy of Sciences, 1986
- Nucleotide Sequence of SRV-1, a Type D Simian Acquired Immune Deficiency Syndrome RetrovirusScience, 1986
- Identification of protein sequence homology by consensus template alignmentJournal of Molecular Biology, 1986
- Nucleotide sequence of the CytR regulatory gene ofE. coliK-12Nucleic Acids Research, 1986
- Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor.Molecular Biology and Evolution, 1985
- Rapid and Sensitive Protein Similarity SearchesScience, 1985