• CombAlign: a code for generati...

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

Title:
CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.
Authors:
Zhou CL; Computational Biology Group, Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 USA.
Source:
Source code for biology and medicine [Source Code Biol Med] 2015 Aug 05; Vol. 10, pp. 9. Date of Electronic Publication: 2015 Aug 05 (Print Publication: 2015).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 101276533 Publication Model: eCollection Cited Medium: Print ISSN: 1751-0473 (Print) Linking ISSN: 17510473 NLM ISO Abbreviation: Source Code Biol Med Subsets: PubMed not MEDLINE
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2006-2020
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Contributed Indexing:
Keywords: Ebola; Matrix protein; Msa; Mssa; Multiple sequence alignment; Multiple structure alignment; Secreted glycoprotein; VP40; sGP
Entry Date(s):
Date Created: 20150807 Date Completed: 20150806 Latest Revision: 20200929
Update Code:
20250114
PubMed Central ID:
PMC4526201
DOI:
10.1186/s13029-015-0039-1
PMID:
26246852
Database:
MEDLINE

Weitere Informationen

Background: In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure.
Results: This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins.
Conclusions: CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.