MDAT- Aligning multiple domain arrangements

Background: Proteins are composed of domains, protein segments that fold independently from the rest of the protein and have a specific function. During evolution the arrangement of domains can change: domains are gained, lost or their order is rearranged. To facilitate the analysis of these changes...

Authors: Kemena, Carsten
Bitard-Feildel, Tristan
Bornberg-Bauer, Erich
Division/Institute:FB 13: Biologie
Document types:Article
Media types:Text
Publication date:2015
Date of publication on miami:28.05.2015
Modification date:16.04.2019
Edition statement:[Electronic ed.]
Source:BMC Bioinformatics 16 (2015) 19, 1-7
Subjects:Domain arrangement; Multiple alignment
DDC Subject:570: Biowissenschaften; Biologie
License:CC BY 4.0
Language:English
Notes:Finanziert durch den Open-Access-Publikationsfonds 2014/2015 der Deutschen Forschungsgemeinschaft (DFG) und der Westfälischen Wilhelms-Universität Münster (WWU Münster).
Format:PDF document
ISSN:1471-2105
URN:urn:nbn:de:hbz:6-09259509297
Permalink:http://nbn-resolving.de/urn:nbn:de:hbz:6-09259509297
Other Identifiers:DOI: doi:10.1186/s12859-014-0442-7
Digital documents:s12859-014-0442-7.pdf

Background: Proteins are composed of domains, protein segments that fold independently from the rest of the protein and have a specific function. During evolution the arrangement of domains can change: domains are gained, lost or their order is rearranged. To facilitate the analysis of these changes we propose the use of multiple domain alignments. Results: We developed an alignment program, called MDAT, which aligns multiple domain arrangements. MDAT extends earlier programs which perform pairwise alignments of domain arrangements. MDAT uses a domain similarity matrix to score domain pairs and aligns the domain arrangements using a consistency supported progressive alignment method. Conclusion: MDAT will be useful for analysing changes in domain arrangements within and between protein families and will thus provide valuable insights into the evolution of proteins and their domains. MDAT is coded in C++, and the source code is freely available for download at http://www.bornberglab.org/pages/mdat