DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
Top Cited Papers
Open Access
- 27 May 2008
- journal article
- Published by Springer Nature in Algorithms for Molecular Biology
- Vol. 3 (1) , 6
- https://doi.org/10.1186/1748-7188-3-6
Abstract
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.Keywords
This publication has 40 references indexed in Scilit:
- Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins familyAlgorithms for Molecular Biology, 2008
- Local Decoding of Sequences and Alignment-Free ComparisonJournal of Computational Biology, 2006
- MAFFT version 5: improvement in accuracy of multiple sequence alignmentNucleic Acids Research, 2005
- Multiple sequence alignment with user-defined constraints at GOBICSBioinformatics, 2004
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- CLUSTAL: a package for performing multiple sequence alignment on a microcomputerPublished by Elsevier ,2003
- T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. ThorntonJournal of Molecular Biology, 2000
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Basic local alignment search toolJournal of Molecular Biology, 1990
- Individual Comparisons by Ranking MethodsBiometrics Bulletin, 1945