Academic Journal
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.
| Τίτλος: | DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. |
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| Συγγραφείς: | Subramanian, Amarendran R., Kaufmann, Michael, Morgenstern, Burkhard |
| Πηγή: | Algorithms for Molecular Biology; 2008, Vol. 3, Special section p1-11, 11p, 1 Diagram, 10 Charts |
| Θεματικοί όροι: | Genetic algorithms, Amino acid sequence, Nucleotide sequence, Heuristic programming, Genomic information retrieval, Computational biology |
| Περίληψη: | Background: DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach. Results: Our new heuristic produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly. The new method is based on a guide tree; to detect possible spurious sequence similarities, it employs a vertex-cover approximation on a conflict graph. We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively. For alignment of nucleic acid sequences, we used BRAliBase II for global alignment and a newly developed database of locally related sequences called DIRM-BASE 1. IRMBASE 2 and DIRMBASE 1 are constructed by implanting highly conserved motives at random positions in long unalignable sequences. Conclusion: On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX. [ABSTRACT FROM AUTHOR] |
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| Βάση Δεδομένων: | Complementary Index |
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