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CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence

Carol L Ecale Zhou1

  • 1Computational Biology Group, Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 USA.

Source Code for Biology and Medicine
|August 7, 2015
PubMed
Summary
This summary is machine-generated.

A new Python code, CombAlign, creates gapped multiple sequence alignments from pairwise alignments. This tool helps identify conserved and divergent regions in related protein structures, improving structural comparisons.

Keywords:
EbolaMatrix proteinMsaMssaMultiple sequence alignmentMultiple structure alignmentSecreted glycoproteinVP40sGP

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Identifying residue-residue correspondences is crucial for comparing related protein structures.
  • Existing tools lack the ability to create one-to-many multiple sequence alignments with gaps in the reference structure.

Purpose of the Study:

  • To develop a novel Python code, CombAlign, for generating one-to-many gapped multiple sequence alignments.
  • To facilitate the comparison of related protein structures by combining pairwise alignments.

Main Methods:

  • CombAlign takes a set of pairwise sequence or structure-based alignments as input.
  • It generates a one-to-many, gapped, multiple structure- or sequence-based alignment (MSSA).

Main Results:

  • CombAlign successfully generated gapped MSSAs for Ebolavirus proteins (VP40 and sGP) against other filoviruses.
  • The generated MSSAs revealed structure-based residue-residue correspondences.
  • Structurally similar and differing regions between Reston Ebolavirus proteins and other filoviruses were identified.

Conclusions:

  • CombAlign is a valuable Python tool for creating gapped MSSAs from pairwise alignments.
  • It aids in distinguishing conserved and divergent structural regions in related proteins.
  • The code is available on GitHub.