The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

Keywords

Multiple sequence alignment, Unix, Sequence alignment, Graphics, Sequence (biology)

References

• Using CLUSTAL for multiple sequence alignments.Desmond G. Higgins, Julie Thompson, Toby J. Gibson — 1996
• Position-based sequence weights.Steven Henikoff, Jorja G. Henikoff — 1994
• Improved sensitivity of profile searches through the use of sequence weights and gap excisionJulie Thompson, Desmond G. Higgins, Toby J. Gibson — 1994
• Amino acid substitution during functionally constrained divergent evolution of protein sequences.S. A. Bennet, Mark A. Cohen, Gastón H. Gonnet — 1994
• Automatic generation of primary sequence patterns from sets of related protein sequences.Randall F. Smith, Temple F. Smith — 1990
• Prediction of protein secondary structure and active sites using the alignment of homologous sequences.Marketa Zvelebil, Geoffrey J. Barton, William R. Taylor — 1987
• ALMA, an editor for large sequence alignmentsSøren Thirup, Niels E. Larsen — 1990
• Motif recognition and alignment for many sequences by comparison of dot-matrices.Martin Vingron, Patrick Argos — 1991
• Weighting in sequence space: a comparison of methods in terms of generalized sequences.Martin Vingron, Peter R. Sibbald — 1993
• MALIGNED: a multiple sequence alignment editorStephen P. Clark — 1992
• Evolutionary divergence plots of homologous proteins.Sophie Brouillet, J.L. Risler, Alain Hénaut — 1992
• Database of homology‐derived protein structures and the structural meaning of sequence alignmentChris Sander, Reinhard Schneider — 1991
• Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.Osamu Gotoh — 1996
• SAGA: sequence alignment by genetic algorithm.Cédric Notredame — 1996
• PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.Ewan Birney, Julie Thompson, Toby J. Gibson — 1996
• A workbench for multiple alignment construction and analysisGregory D. Schuler, Stephen F. Altschul, David J. Lipman — 1991
• 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
• SOMAP: a novel interactive approach to multiple protein sequences alignmentDavid Parry-Smith, Teresa K. Attwood — 1991
• HOMED: a homologous sequence editorPeter A. Stockwell, George B. Petersen — 1987
• A new approach for displaying identities and differences among aligned amino acid sequencesAndreas Friemann, Stefan Schmitz — 1992

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• PAL: A Perl Script for Rapidly Identifying the Active Site of Large Protein FamiliesAndres A. Larrea, Pablo Ledesma Larrea — 2007
• Phylogenetic Approaches to Natural Product Structure PredictionNadine Ziemert, Paul R. Jensen — 2012
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• Phenotypic and genotypic characterization of Thai oral streptococci, lactobacilli and pediococci.J. Kuvatanasuchati, Nitcha Chamroensaksri, Somboon Tanasupawat — 2012
• Population genetics and evolutionary history of some deep-sea demersal fishes from the Azores - North AtlanticMaria Ana Aboim — 2005
• Cloning and functional analysis of a cDNA encoding Ginkgo biloba farnesyl diphosphate synthase.Peng Wang, Zhihua Liao, Liang Guo — 2004
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• Cell-cycle regulatory proteins Hsl7p/Skb1p belong to the protein methyltransferase superfamily.Ringkas Sitepu — 2000
• Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4‐cytosine specific M.NgoMXV and nonfunctional 5‐cytosine‐type M.NgoMorf2PMonika Radlińska, Janusz M. Bujnicki, Andrzej Piekarowicz — 1999
• Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.Stephen J. Mraz — 2000
• Characterization of five novel human genes in the 11q13-q22 region.みち子 前野, Michiko Maeno — 2000

Related papers

• Alignment of protein sequences by their profilesMarc A. Martı́-Renom, M. S. Madhusudhan, Andrej Šali — 2004
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• Homology-extended sequence alignmentV. A. Simossis — 2005
• A comprehensive comparison of multiple sequence alignment programsJulie Thompson, Frédéric Plewniak, Olivier Poch — 1999
• Parallel genetic algorithm for performance-driven sequence alignmentL. A. Anbarasu, Vijayaraghava Seshadri Sundararajan, P. Narayanasamy — 2001
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• Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residuesYue Lu, Sing-Hoi Sze — 2008
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