title: CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.
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.
authors.affiliation: Computational Biology Group, Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 USA.
authors.forename: Carol L Ecale
authors.initials: CL
authors.lastname: Zhou
keywords: Ebola; Matrix protein; Msa; Mssa; Multiple sequence alignment; Multiple structure alignment; Secreted glycoprotein; VP40; sGP