Improving the sensitivity of the sequence profile method.

Détails

ID Serval
serval:BIB_748EC2FE8DA4
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Improving the sensitivity of the sequence profile method.
Périodique
Protein Science
Auteur(s)
Lüthy R., Xenarios I., Bucher P.
ISSN
0961-8368 (Print)
ISSN-L
0961-8368
Statut éditorial
Publié
Date de publication
1994
Volume
3
Numéro
1
Pages
139-146
Langue
anglais
Résumé
The 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 position-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 (Sibbald 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 Acad 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.
Mots-clé
Amino Acid Sequence, Globins/chemistry, Heat-Shock Proteins/chemistry, Molecular Sequence Data, Proto-Oncogene Proteins pp60(c-src)/chemistry, Sensitivity and Specificity, Sequence Analysis/methods, Sequence Analysis/statistics & numerical data, Sequence Homology, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
18/10/2012 10:20
Dernière modification de la notice
08/05/2019 20:28
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