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Open Access Methodology article

Reticular alignment: A progressive corner-cutting method for multiple sequence alignment

Adrienn Szabó12, Ádám Novák34*, István Miklós15 and Jotun Hein3

Author Affiliations

1 Computer and Automation Research Institute, Hungarian Academy of Sciences, Lágymányosi u. 11., 1111 Budapest, Hungary

2 Eötvös Loránd University, Faculty of Informatics, Pázmány Péter sétány 1/c., 1117 Budapest, Hungary

3 Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK

4 Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, OX1 3QU Oxford, UK

5 Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Reáltanoda u. 13-15., 1053 Budapest, Hungary

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BMC Bioinformatics 2010, 11:570  doi:10.1186/1471-2105-11-570

Published: 23 November 2010

Abstract

Background

In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments are represented with a network to store them and use them during the progressive alignment in an efficient way. The program contains a threshold parameter on which the size of the network depends. The larger the threshold parameter and thus the network, the deeper the search in the alignment space for better scored alignments.

Results

We implemented the program in the Java programming language, and tested it on the BAliBASE database. Reticular Alignment can outperform ClustalW even if a very simple scoring scheme (BLOSUM62 and affine gap penalty) is implemented and merely the threshold value is increased. However, this set-up is not sufficient for outperforming other cutting-edge alignment methods. On the other hand, the reticular alignment search strategy together with sophisticated scoring schemes (for example, differentiating gap penalties for hydrophobic and hydrophylic amino acids) overcome FSA and in some accuracy measurement, even MAFFT. The program is available from http://phylogeny-cafe.elte.hu/RetAlign/ webcite

Conclusions

Reticular alignment is an efficient search strategy for finding accurate multiple alignments. The highest accuracy achieved when this searching strategy is combined with sophisticated scoring schemes.