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MultiSeq: unifying sequence and structure data for evolutionary analysis.

Elijah Roberts1, John Eargle, Dan Wright

  • 1Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. erobert3@scs.uiuc.edu

BMC Bioinformatics
|August 18, 2006
PubMed
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MultiSeq is a bioinformatics environment for analyzing protein and nucleic acid sequence and structure data. It uses evolutionary methods to identify evolutionary profiles and a minimal basis set of proteins.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Vast amounts of bioinformatic data (sequences, structures) pose challenges for correlation analysis.
  • Integrating information science, visualization, mathematics, and biology is crucial for addressing these challenges.
  • Existing tools struggle to efficiently organize and analyze diverse biological data.

Purpose of the Study:

  • To present MultiSeq, a unified bioinformatics environment for analyzing sequence and structure data.
  • To enable the organization, display, alignment, and analysis of protein and nucleic acid data.
  • To support evolutionary biology frameworks and flexible usage patterns.

Main Methods:

  • Developed MultiSeq, a unified bioinformatics analysis environment.

Related Experiment Videos

  • Incorporated predefined metadata and ontological mappings for evolutionary analysis.
  • Implemented a novel algorithm for generating evolutionary profiles using multidimensional QR factorization.
  • Utilized an electronic notebook for user-adjustable classifications.

    • Main Results:

    • MultiSeq allows integrated analysis of sequence and structure data for proteins and nucleic acids.
    • A new algorithm generates complete evolutionary profiles, representing molecular phylogenetic tree topology.
    • The method removes redundancy in alignments and identifies a minimal basis set of sequences spanning evolutionary space.
    • The approach aids in understanding evolutionary relationships within homologous protein groups.

    Conclusions:

    • MultiSeq is a significant extension of VMD's Multiple Alignment tool.
    • The software is freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics.
    • MultiSeq is integrated into VMD version 1.8.5 and later, with download and usage details available online.