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

Zhou CL - Source Code Biol Med (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

ABSTRACT

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.

No MeSH data available.


Multiple structure-based sequence alignment (MSSA) of Reston Ebolavirus VP40 model (reference) aligned with VP40 models from four Ebolaviruses and one Marburgvirus species. Pairwise TM-align alignments were combined using combAlign.py
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Fig1: Multiple structure-based sequence alignment (MSSA) of Reston Ebolavirus VP40 model (reference) aligned with VP40 models from four Ebolaviruses and one Marburgvirus species. Pairwise TM-align alignments were combined using combAlign.py

Mentions: The use and utility of CombAlign was demonstrated by generating a gapped MSSA using a structure model of the matrix protein (VP40) from Reston Ebolavirus (as the reference structure) and pairwise alignments between the reference and structure models of the VP40s from Bundibugyo, Sudan, Tai Forest, and Zaire Ebolaviruses and Marburg Marburgvirus (Fig. 1). The gapped MSSA revealed structure-based residue-residue correspondences between Reston Ebolavirus VP40 and each of the other VP40 proteins, which enabled identification of structurally similar versus differing regions in Reston compared to each of the closely related proteins.Fig. 1


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

Zhou CL - Source Code Biol Med (2015)

Multiple structure-based sequence alignment (MSSA) of Reston Ebolavirus VP40 model (reference) aligned with VP40 models from four Ebolaviruses and one Marburgvirus species. Pairwise TM-align alignments were combined using combAlign.py
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526201&req=5

Fig1: Multiple structure-based sequence alignment (MSSA) of Reston Ebolavirus VP40 model (reference) aligned with VP40 models from four Ebolaviruses and one Marburgvirus species. Pairwise TM-align alignments were combined using combAlign.py
Mentions: The use and utility of CombAlign was demonstrated by generating a gapped MSSA using a structure model of the matrix protein (VP40) from Reston Ebolavirus (as the reference structure) and pairwise alignments between the reference and structure models of the VP40s from Bundibugyo, Sudan, Tai Forest, and Zaire Ebolaviruses and Marburg Marburgvirus (Fig. 1). The gapped MSSA revealed structure-based residue-residue correspondences between Reston Ebolavirus VP40 and each of the other VP40 proteins, which enabled identification of structurally similar versus differing regions in Reston compared to each of the closely related proteins.Fig. 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

ABSTRACT

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.

No MeSH data available.