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PMID: 16914055 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

MultiSeq: unifying sequence and structure data for evolutionary analysis.

BMC bioinformatics ·Vol. 7 ·2006-08-16 ·Pages 382

Roberts E, Eargle J, Wright D, Luthey-Schulten Z

Abstract

Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/

MeSH Terms
Algorithms Computational Biology/methods Computer Graphics Computer Simulation DNA/chemistry Databases, Genetic Evolution, Molecular Models, Molecular Nucleic Acid Conformation Phylogeny Protein Conformation Proteins/chemistry,classification,genetics Sequence Alignment Sequence Analysis, DNA Sequence Analysis, Protein Sequence Homology, Nucleic Acid Software Structural Homology, Protein
Chemicals
Proteins DNA
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Roberts Elijah
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. [email protected]
Eargle John
Wright Dan
Luthey-Schulten Zaida
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-7-382
Email
[email protected]
Published
2006-08-16
Epub
2006-00-16
Pages
382
Language
English
Region
England
NLM ID
100965194
PMCID
PMC1586216
Subset
IM
Grants
NCRR NIH HHS · P41 RR005969 · United States
NIGMS NIH HHS · T32 GM008276 · United States
NCRR NIH HHS · PHS2P41RR05969 · United States
NIGMS NIH HHS · PHS5T32GM08276 · United States
External Links
PubMed source DOI: 10.1186/1471-2105-7-382 PMC Full Text View journal details
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