Abstract
BackgroundProteins 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.ResultsWe 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.ConclusionMDAT 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0442-7) contains supplementary material, which is available to authorized users.
Highlights
Proteins are composed of domains, protein segments that fold independently from the rest of the protein and have a specific function
Domain similarity matrix The Pfam database provides some rough information on domain homology based on a range of various information evaluated manually [19,20]
We show that using multiple domain alignment (MDA) themselves has its merits
Summary
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. The number of known arrangements, the combination of domains in a protein, is much higher and steadily and rapidly increasing with more genomes being sequenced [7]. These arrangements evolve over time as domains can be lost, new ones gained and domains are reordered, mostly by gene fusion and terminal domain losses.
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