DOI: 10.1002/pro.5560030118. Improving the sensitivity of the sequence profile method

Improving the sensitivity of the sequence profile method

10.1002/pro.5560030118

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractThe sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355‐4358) is a powerful tool to detect distant relationships between amino acid sequences. A profile is a table of posi‐tion‐specific scores and gap penalties, providing a generalized description of a protein motif, which can be used for sequence alignments and database searches instead of an individual sequence. A sequence profile is derived from a multiple sequence alignment. We have found 2 ways to improve the sensitivity of sequence profiles: (1) Sequence weights: Usage of individual weights for each sequence avoids bias toward closely related sequences. These weights are automatically assigned based on the distance of the sequences using a published procedure (Sib‐bald PR, Argos P, 1990, J Mol Biol 216:813‐818). (2) Amino acid substitution table: In addition to the alignment, the construction of a profile also needs an amino acid substitution table. We have found that in some cases a new table, the BLOSUM45 table (Henikoff S, Henikoff JG, 1992, Proc Natl Acud Sci USA 89:10915‐10919), is more sensitive than the original Dayhoff table or the modified Dayhoff table used in the current implementation. Profiles derived by the improved method are more sensitive and selective in a number of cases where previous methods have failed to completely separate true members from false positives.

Bibliography

LÃ¼thy, R., Xenarios, I., & Bucher, P. (1994). Improving the sensitivity of the sequence profile method. Protein Science, 3(1), 139â146. Portico.

Authors 3

Roland Lüthy (first)
Ioannis Xenarios (additional)
Philipp Bucher (additional)

References 17 Referenced 92

10.1016/0022-2836(89)90234-9
10.1093/nar/20.suppl.2013
10.1093/nar/20.suppl.2019
10.1016/0014-5793(89)81818-6
{'key': 'e_1_2_1_6_1', 'first-page': '345', 'volume-title': 'Atlas of protein sequence and structure', 'author': 'Dayhoff MO', 'year': '1978'} / Atlas of protein sequence and structure by Dayhoff MO (1978)
10.1093/nar/12.1Part1.387
10.1093/nar/14.16.6745 / Nucleic Acids Res / Sigma factors from E. coli, B. subtilis, phage SP01 and phage T4 are homologous proteins by Gribskov M (1986)
10.1016/0076-6879(90)83011-W
10.1073/pnas.84.13.4355
10.1073/pnas.89.22.10915
10.1002/j.1460-2075.1985.tb03847.x
10.1016/0022-2836(80)90373-3
10.1016/0092-8674(92)90504-6
10.1007/BF00160214
10.1016/S0022-2836(99)80003-5
10.1073/pnas.87.1.118
10.1016/0196-8858(81)90046-4

Dates

Type	When
Created	15 years, 1 month ago (July 12, 2010, 4:34 a.m.)
Deposited	1 year, 10 months ago (Oct. 24, 2023, 3:41 a.m.)
Indexed	4 months, 4 weeks ago (March 27, 2025, 8:34 a.m.)
Issued	31 years, 7 months ago (Jan. 1, 1994)
Published	31 years, 7 months ago (Jan. 1, 1994)
Published Online	16 years, 7 months ago (Dec. 31, 2008)
Published Print	31 years, 7 months ago (Jan. 1, 1994)

Funders 0

None

BibTeX

@article{L_thy_1994, title={Improving the sensitivity of the sequence profile method}, volume={3}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560030118}, DOI={10.1002/pro.5560030118}, number={1}, journal={Protein Science}, publisher={Wiley}, author={Lüthy, Roland and Xenarios, Ioannis and Bucher, Philipp}, year={1994}, month=jan, pages={139–146} }

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