Flexible mapping of homology onto structure with Homolmapper

<p>Abstract</p> <p>Background</p> <p>Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular...

Full description

Bibliographic Details
Main Authors: Lagarias J Clark, Rockwell Nathan C
Format: Article
Language:English
Published: BMC 2007-04-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/8/123
id doaj-422dc91183434d959bf85253a27fcef2
record_format Article
spelling doaj-422dc91183434d959bf85253a27fcef22020-11-24T21:30:05ZengBMCBMC Bioinformatics1471-21052007-04-018112310.1186/1471-2105-8-123Flexible mapping of homology onto structure with HomolmapperLagarias J ClarkRockwell Nathan C<p>Abstract</p> <p>Background</p> <p>Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine.</p> <p>Results</p> <p>We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs.</p> <p>Conclusion</p> <p>Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at <url>http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm</url>.</p> http://www.biomedcentral.com/1471-2105/8/123
collection DOAJ
language English
format Article
sources DOAJ
author Lagarias J Clark
Rockwell Nathan C
spellingShingle Lagarias J Clark
Rockwell Nathan C
Flexible mapping of homology onto structure with Homolmapper
BMC Bioinformatics
author_facet Lagarias J Clark
Rockwell Nathan C
author_sort Lagarias J Clark
title Flexible mapping of homology onto structure with Homolmapper
title_short Flexible mapping of homology onto structure with Homolmapper
title_full Flexible mapping of homology onto structure with Homolmapper
title_fullStr Flexible mapping of homology onto structure with Homolmapper
title_full_unstemmed Flexible mapping of homology onto structure with Homolmapper
title_sort flexible mapping of homology onto structure with homolmapper
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2007-04-01
description <p>Abstract</p> <p>Background</p> <p>Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine.</p> <p>Results</p> <p>We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs.</p> <p>Conclusion</p> <p>Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at <url>http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm</url>.</p>
url http://www.biomedcentral.com/1471-2105/8/123
work_keys_str_mv AT lagariasjclark flexiblemappingofhomologyontostructurewithhomolmapper
AT rockwellnathanc flexiblemappingofhomologyontostructurewithhomolmapper
_version_ 1725964062461788160