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MDAT- Aligning multiple domain arrangements.

Kemena C, Bitard-Feildel T, Bornberg-Bauer E - BMC Bioinformatics (2015)

Bottom Line: We developed an alignment program, called MDAT, which aligns multiple domain arrangements.MDAT extends earlier programs which perform pairwise alignments of domain arrangements.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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, Germany. c.kemena@uni-muenster.de.

ABSTRACT

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 .

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Related in: MedlinePlus

Workflow of the MDA2MSA algorithm. Step 1: Sequences with identical domain arrangements (a) are split according to domain boundaries (b). Then each part is separately aligned (c) and finally all parts are merged back together (d) into a single alignment. Step 2: The MDA (a) is used as a guide. The sequences are split into parts according to the MDA (b). Cuts are performed at the borders of aligned domains resulting in 5 parts. Each pair of sequence segments can now be aligned separately. In case unaligned domains occur in the MDA (part 3), the dynamic programming algorithm is changed such that it maintains the order of domains (c). The striped area represents the area that is not calculated because the MDA forbids the alignment of the two domains.
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Fig4: Workflow of the MDA2MSA algorithm. Step 1: Sequences with identical domain arrangements (a) are split according to domain boundaries (b). Then each part is separately aligned (c) and finally all parts are merged back together (d) into a single alignment. Step 2: The MDA (a) is used as a guide. The sequences are split into parts according to the MDA (b). Cuts are performed at the borders of aligned domains resulting in 5 parts. Each pair of sequence segments can now be aligned separately. In case unaligned domains occur in the MDA (part 3), the dynamic programming algorithm is changed such that it maintains the order of domains (c). The striped area represents the area that is not calculated because the MDA forbids the alignment of the two domains.

Mentions: An MDA can be used to guide the MSA alignment process. MDAT uses a similar approach to the one described in Dialign-Pfam. Blocks of domains are used as anchor points to limit the search space and thereby increasing the speed of the alignment calculation. Furthermore, using the MDA as an anchor, guarantees that the correct domains are aligned with each other (see Results and discussion). Unlike Dialign-Pfam, MDAT uses a completely automatic approach and because we use the MDA as guide, the anchors do not need to be of a single domain type. The MDA is used as a backbone for the MSA construction. This process can be divided into two major steps. In the first step, sequences with identical domain arrangements are aligned, in the second the alignments of the first step are aligned with each other. This two-step process is shown in Figure 4.Figure 4


MDAT- Aligning multiple domain arrangements.

Kemena C, Bitard-Feildel T, Bornberg-Bauer E - BMC Bioinformatics (2015)

Workflow of the MDA2MSA algorithm. Step 1: Sequences with identical domain arrangements (a) are split according to domain boundaries (b). Then each part is separately aligned (c) and finally all parts are merged back together (d) into a single alignment. Step 2: The MDA (a) is used as a guide. The sequences are split into parts according to the MDA (b). Cuts are performed at the borders of aligned domains resulting in 5 parts. Each pair of sequence segments can now be aligned separately. In case unaligned domains occur in the MDA (part 3), the dynamic programming algorithm is changed such that it maintains the order of domains (c). The striped area represents the area that is not calculated because the MDA forbids the alignment of the two domains.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384290&req=5

Fig4: Workflow of the MDA2MSA algorithm. Step 1: Sequences with identical domain arrangements (a) are split according to domain boundaries (b). Then each part is separately aligned (c) and finally all parts are merged back together (d) into a single alignment. Step 2: The MDA (a) is used as a guide. The sequences are split into parts according to the MDA (b). Cuts are performed at the borders of aligned domains resulting in 5 parts. Each pair of sequence segments can now be aligned separately. In case unaligned domains occur in the MDA (part 3), the dynamic programming algorithm is changed such that it maintains the order of domains (c). The striped area represents the area that is not calculated because the MDA forbids the alignment of the two domains.
Mentions: An MDA can be used to guide the MSA alignment process. MDAT uses a similar approach to the one described in Dialign-Pfam. Blocks of domains are used as anchor points to limit the search space and thereby increasing the speed of the alignment calculation. Furthermore, using the MDA as an anchor, guarantees that the correct domains are aligned with each other (see Results and discussion). Unlike Dialign-Pfam, MDAT uses a completely automatic approach and because we use the MDA as guide, the anchors do not need to be of a single domain type. The MDA is used as a backbone for the MSA construction. This process can be divided into two major steps. In the first step, sequences with identical domain arrangements are aligned, in the second the alignments of the first step are aligned with each other. This two-step process is shown in Figure 4.Figure 4

Bottom Line: We developed an alignment program, called MDAT, which aligns multiple domain arrangements.MDAT extends earlier programs which perform pairwise alignments of domain arrangements.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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, Germany. c.kemena@uni-muenster.de.

ABSTRACT

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 .

Show MeSH
Related in: MedlinePlus