skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A Maximum Entropy Formalism for Disentangling Chains of Correlated Sequence Positions

Abstract

Covariation analysis of sets of aligned sequences of protein molecules is successful in certain instances in elucidating certain structural and functional links, but in general, pairs of sites displaying highly covarying mutations in protein sequences do not necessarily correspond to sites that are spatially close in the protein structure. In contrast, covariation analysis of sets of aligned sequences for RNA molecules is relatively successful in elucidating RNA secondary structure, as well as some aspects of tertiary structure. The goals of this paper are to (1) present the problem, (2) develop the mathematical formalism for solving the problem, and (3) validate the resulting algorithms on simulated data. Extensive application to biological sequences will be presented elsewhere.

Authors:
; ; ;
Publication Date:
Research Org.:
Los Alamos National Lab., NM (US)
Sponsoring Org.:
USDOE Office of Energy Research (ER) (US)
OSTI Identifier:
763147
Report Number(s):
LA-UR-98-1094
TRN: AH200103%%506
DOE Contract Number:
W-7405-ENG-36
Resource Type:
Technical Report
Resource Relation:
Other Information: Published in Montreal Canada, Journal Intelligent Systems in Molecular Biology '98; PBD: 3 Aug 1998
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; CHAINS; ENTROPY; FUNCTIONALS; MUTATIONS; PROTEIN STRUCTURE; PROTEINS; RNA; CORRELATED MUTATIONS; MUTUAL INFORMATION; MAXIMUM ENTROPY

Citation Formats

Lapedes, A.S., Giraud, B.G., Liu, L.C., and Stormo, G.D. A Maximum Entropy Formalism for Disentangling Chains of Correlated Sequence Positions. United States: N. p., 1998. Web. doi:10.2172/763147.
Lapedes, A.S., Giraud, B.G., Liu, L.C., & Stormo, G.D. A Maximum Entropy Formalism for Disentangling Chains of Correlated Sequence Positions. United States. doi:10.2172/763147.
Lapedes, A.S., Giraud, B.G., Liu, L.C., and Stormo, G.D. Mon . "A Maximum Entropy Formalism for Disentangling Chains of Correlated Sequence Positions". United States. doi:10.2172/763147. https://www.osti.gov/servlets/purl/763147.
@article{osti_763147,
title = {A Maximum Entropy Formalism for Disentangling Chains of Correlated Sequence Positions},
author = {Lapedes, A.S. and Giraud, B.G. and Liu, L.C. and Stormo, G.D.},
abstractNote = {Covariation analysis of sets of aligned sequences of protein molecules is successful in certain instances in elucidating certain structural and functional links, but in general, pairs of sites displaying highly covarying mutations in protein sequences do not necessarily correspond to sites that are spatially close in the protein structure. In contrast, covariation analysis of sets of aligned sequences for RNA molecules is relatively successful in elucidating RNA secondary structure, as well as some aspects of tertiary structure. The goals of this paper are to (1) present the problem, (2) develop the mathematical formalism for solving the problem, and (3) validate the resulting algorithms on simulated data. Extensive application to biological sequences will be presented elsewhere.},
doi = {10.2172/763147},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Aug 03 00:00:00 EDT 1998},
month = {Mon Aug 03 00:00:00 EDT 1998}
}

Technical Report:

Save / Share: