DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

Keywords

Multiple sequence alignment, Computer science, Alignment-free sequence analysis, Smith–Waterman algorithm, Sequence alignment

References

• OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracyGPS Raghava, Stephen M. J. Searle, Patrick C. Audley — 2003
• PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid SequencesJoshua Shulman, Michael Brudno, Serafim Batzoglou — 2004
• Biological sequence analysisTerence P. Speed — 2003
• An assessment of gene prediction accuracy in large DNA sequences.Roderic Guigó, Pankaj Agarwal, Josep F. Abril — 2000
• DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignmentBurkhard Morgenstern — 1999
• Quality assessment of multiple alignment programsTimo Lassmann, Erik L. L. Sonnhammer — 2002
• Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski — 1993
• Multiple sequence alignment by consensus.Michael S. Waterman — 1986
• Multiple sequence alignment with hierarchical clustering.F. Corpet — 1988
• MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequencesEric Depiereux, Ernest Feytmans — 1992
• Multiple DNA and protein sequence alignment based on segment-to-segment comparison.Burkhard Morgenstern, Andreas Dress, Thomas Werner — 1996
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.Saul B. Needleman, Christian D. Wunsch — 1970
• A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequencesBurkhard Morgenstern — 2002
• Rose: generating sequence familiesJens Stoye, Dorothea Evers, Folker Meyer — 1998
• Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.Osamu Gotoh — 1996
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Julie Thompson, Desmond G. Higgins, Toby J. Gibson — 1994
• Align-m-a new algorithm for multiple alignment of highly divergent sequencesIvo Van Walle, Ignace Lasters, Lode Wyns — 2004
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.R. C. Edgar — 2004
• A comprehensive comparison of multiple sequence alignment programsJulie Thompson, Frédéric Plewniak, Olivier Poch — 1999
• Multiple sequence alignment using partial order graphsChristopher Lee, Catherine S. Grasso, Mark Sharlow — 2002

Cited by

• Automated Genome-Wide Protein Domain ExplorationBhanu Rekepalli — 2007
• Rapid similarity search of proteins using alignments of domain arrangementsNicolas Terrapon, January Weiner, Sonja Grath — 2014
• Heuristiques pour la résolution du problème d'alignement multiple. (Heuristics for the multiple alignment problem)Vincent Derrien — 2008
• RNA-Alignments und RNA-Struktur in silicoAndreas Wilm — 2006
• Discovering critical residues in glutathione reductaseDonnie Berkholz — 2006
• Molecular and biochemical characterisation of novel glycosyltransferases in Mycobacterium tuberculosisHelen L. Birch — 2011
• Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupinsFrédéric Mahé — 2009
• Multiple sequence alignment using particle swarm optimizationFabien Bernard Roman Zablocki — 2008
• Improvement in Speed and Accuracy of Multiple Sequence Alignment Program PRIMEShinsuke Yamada, Osamu Goto, Hayato Yamana — 2009
• Biologically relevant multiple sequence alignmentHyrum Carroll — 2008
• Pathogenesis-related proteins: phylogenetic characterizationN. Scherer — 2010
• Biosynthese von Arabinan - ein komplexer Bestandteil der Zellwand in CorynebacterianeaeMathias Seidel — 2007
• Comprehensive comparative analysis of kinesins in photosynthetic eukaryotesDale N. Richardson, Mark P. Simmons, Anireddy S. N. Reddy — 2006
• Improvement in the accuracy of multiple sequence alignment program MAFFT.Kazutaka Katoh, Kei‐ichi Kuma, Takashi Miyata — 2005
• Dissecting multiple sequence alignment methodsTobias Rausch — 2010
• The accuracy of several multiple sequence alignment programs for proteinsPaulo Nuin, Zhouzhi Wang, Elisabeth R.M. Tillier — 2006
• A phylogenomic perspective on annelid evolution with emphasis on the evolution of bloodfeeding in leeches (Clitellata, Hirudinida)Sebastian Kvist — 2012
• Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap costShinsuke Yamada, Osamu Gotoh, Hayato Yamana — 2006
• Multiple sequence alignment for phylogenetic purposesDavid A. Morrison — 2006
• Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative SplicingDale N. Richardson, Mark F. Rogers, Adam Labadorf — 2011

Related papers

• Alignment of protein sequences by their profilesMarc A. Martı́-Renom, M. S. Madhusudhan, Andrej Šali — 2004
• Homology-extended sequence alignmentV. A. Simossis — 2005
• Pairwise alignment of nucleotide sequences using maximal exact matchesArash Bayat, Bruno Gaëta, Aleksandar Ignjatović — 2019
• Biological Sequence Alignment for Bioinformatics Applications Using MATLABSonali Vijan — 2011
• ALIGN_MTX - An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignmentBoris Vishnepolsky, Malak Pirtskhalava — 2009
• A comprehensive comparison of multiple sequence alignment programsJulie Thompson, Frédéric Plewniak, Olivier Poch — 1999
• Dynamic use of multiple parameter sets in sequence alignmentXiaoqiu Huang, Douglas L. Brutlag — 2006
• Multithreaded implementation of a biomolecular sequence alignment algorithm-software/information technologyWeiwei Gao, Sanzheng Qiao — 2000