Correlated mutations in protein sequences: Phylogenetic and structural effects

PDF Version Also Available for Download.

Description

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. Covariation analysis of sets of aligned sequences for 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 this paper the authors identify two reasons why naive use of covariation analysis for protein sequences fails to reliably indicate sequence positions that are ... continued below

Physical Description

22 p.

Creation Information

Lapedes, A. S.; Giraud, B. G.; Liu, L. C. & Stormo, G. D. December 1998.

Context

This report is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this report can be viewed below.

Who

People and organizations associated with either the creation of this report or its content.

Authors

  • Lapedes, A. S. Los Alamos National Lab., NM (United States). Theoretical Div.
  • Giraud, B. G. C.E.N. Saclay, Gif/Yvette (France). Service Physique Theorique
  • Liu, L. C. Los Alamos National Lab., NM (United States). Theoretical Div.
  • Stormo, G. D. Univ. of Colorado, Boulder, CO (United States). Dept. of Molecular, Cellular and Developmental Biology

Sponsor

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this report. Follow the links below to find similar items on the Digital Library.

Description

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. Covariation analysis of sets of aligned sequences for 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 this paper the authors identify two reasons why naive use of covariation analysis for protein sequences fails to reliably indicate sequence positions that are spatially proximate. The first reason involves the bias introduced in calculation of covariation measures due to the fact that biological sequences are generally related by a non-trivial phylogenetic tree. The authors present a null-model approach to solve this problem. The second reason involves linked chains of covariation which can result in pairs of sites displaying significant covariation even though they are not spatially proximate. They present a maximum entropy solution to this classic problem of causation versus correlation. The methodologies are validated in simulation.

Physical Description

22 p.

Notes

OSTI as DE99000640

Source

  • AMS/SIAM conference on statistics in molecular biology, Seattle, WA (United States), Jul 1997

Language

Item Type

Identifier

Unique identifying numbers for this report in the Digital Library or other systems.

  • Other: DE99000640
  • Report No.: LA-UR--98-1091
  • Report No.: CONF-9707181--
  • Grant Number: W-7405-ENG-36
  • DOI: 10.2172/296863 | External Link
  • Office of Scientific & Technical Information Report Number: 296863
  • Archival Resource Key: ark:/67531/metadc682186

Collections

This report is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

What responsibilities do I have when using this report?

When

Dates and time periods associated with this report.

Creation Date

  • December 1998

Added to The UNT Digital Library

  • July 25, 2015, 2:20 a.m.

Description Last Updated

  • Feb. 25, 2016, 2:25 p.m.

Usage Statistics

When was this report last used?

Yesterday: 0
Past 30 days: 1
Total Uses: 3

Interact With This Report

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

International Image Interoperability Framework

IIF Logo

We support the IIIF Presentation API

Lapedes, A. S.; Giraud, B. G.; Liu, L. C. & Stormo, G. D. Correlated mutations in protein sequences: Phylogenetic and structural effects, report, December 1998; New Mexico. (digital.library.unt.edu/ark:/67531/metadc682186/: accessed May 25, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.