A min-cut algorithm for the consistency problem in multiple sequence alignment
Open Access
- 25 February 2010
- journal article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 26 (8) , 1015-1021
- https://doi.org/10.1093/bioinformatics/btq082
Abstract
Motivation: Multiple sequence alignments can be constructed on the basis of pairwise local sequence similarities. This approach is rather flexible and can combine the advantages of global and local alignment methods. The restriction to pairwise alignments as building blocks, however, can lead to misalignments since weak homologies may be missed if only pairs of sequences are compared.Keywords
This publication has 34 references indexed in Scilit:
- Upcoming challenges for multiple sequence alignment methods in the high-throughput eraBioinformatics, 2009
- Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins familyAlgorithms for Molecular Biology, 2008
- DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignmentAlgorithms for Molecular Biology, 2008
- Multiple sequence alignment for phylogenetic purposesAustralian Systematic Botany, 2006
- MAFFT version 5: improvement in accuracy of multiple sequence alignmentNucleic Acids Research, 2005
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. ThorntonJournal of Molecular Biology, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Motif recognition and alignment for many sequences by comparison of dot-matricesJournal of Molecular Biology, 1991