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Multiple sequence alignment with the Clustal series of programs

R. Chenna
2003 Nucleic Acids Research  
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees.  ...  The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs.  ...  ACKNOWLEDGEMENTS We thank the many Clustal users who have provided feedback, bug reports and feature requests.  ... 
doi:10.1093/nar/gkg500 pmid:12824352 pmcid:PMC168907 fatcat:shatrsb3jnbaxelpjoaf5vm6ii

Multiple sequence alignment with Clustal X

François Jeanmougin, Julie D. Thompson, Manolo Gouy, Desmond G. Higgins, Toby J. Gibson
1998 TIBS -Trends in Biochemical Sciences. Regular ed  
We thank former developers for their input and the Clustal users for their informative feedback.  ...  Acknowledgements Clustal development has been supported by Trinity College, Dublin, the EMBL and ICGEB, Strasbourg.  ...  The Clustal series of programs are widely used for multiple alignment and for preparing phylogenetic trees.  ... 
doi:10.1016/s0968-0004(98)01285-7 pmid:9810230 fatcat:l7zrqgthmve7bizfxrkx4wveza

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Julie D. Thompson, Desmond G. Higgins, Toby J. Gibson
1994 Nucleic Acids Research  
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences.  ...  Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned.  ...  Finally, we thank all of the people who have been involved with various CLUSTAL programs over the years, namely Paul Sharp, Rainer Fuchs and Alan Bleasby.  ... 
doi:10.1093/nar/22.22.4673 pmid:7984417 pmcid:PMC308517 fatcat:bxks5rxhmfej7gioz3xl22lafy

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

J. Thompson
1997 Nucleic Acids Research  
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W.  ...  New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment  ...  We thank the many users of CLUSTAL W who have reported bugs/suggestions, and those who beta tested CLUSTAL X.  ... 
doi:10.1093/nar/25.24.4876 pmid:9396791 pmcid:PMC147148 fatcat:xangfdvcvna6ljbeqhvgwney6a

Assessing the efficiency of multiple sequence alignment programs

Fabiano Sviatopolk-Mirsky Pais, Patrícia de Ruy, Guilherme Oliveira, Roney Coimbra
2014 Algorithms for Molecular Biology  
Conclusions: Based on the results presented herein, all four programs Probcons, T-Coffee, Probalign and MAFFT are well recommended for better accuracy of multiple sequence alignments.  ...  Whenever sequences with large N/C terminal extensions were present in the BAliBASE suite, Probalign, MAFFT and also CLUSTAL OMEGA outperformed Probcons and T-Coffee.  ...  We evaluated the alignment accuracy and computational cost of nine different multiple sequence alignment programs with the BAliBASE dataset and discuss the relevance of some implementations embedded in  ... 
doi:10.1186/1748-7188-9-4 pmid:24602402 pmcid:PMC4015676 fatcat:y7sd7t5j4bc7lfwwayz2t5gkta

ETools: Tools to Handle Biological Sequences and Alignments for Evolutionary Studies

Toshinori Endo, Soichi Ogishima, Hiroshi Tanaka
2002 Genome Informatics Series  
Clustal W 1.82 was used for construction of primary multiple alignments and the finishing the refined multiple alignments.  ...  Essentially it follows the four-steps: 1) preparation of the sequence listings for multiple alignment by homology search (BLAST), 2) primary multiple alignment (Clustal W), 3) member sequence validation  ... 
doi:10.11234/gi1990.13.543 fatcat:q7emips54rchzovksmlatttkq4

Creation and Analysis of Protein Multiple Sequence Alignments [chapter]

Geoffrey J. Barton
2002 Methods of biochemical analysis  
The program uses a series of different pair-score matrices, biases the location of gaps, and allows you to realign a set of aligned sequences to refine the alignment.  ...  With the exception of manual editing and visualization, CLUSTAL W contains most of the tools that are needed to build and refine a multiple sequence alignment.  ...  This series of steps produces a ''clean alignment'' for inspection.  ... 
doi:10.1002/0471223921.ch9 fatcat:brl5cvk54rgdtbuiu5douewaxa

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus, W. Li, R. Lopez, H. McWilliam, M. Remmert, J. Soding, J. D. Thompson, D. G. Higgins
2014 Molecular Systems Biology  
Multiple Sequence Alignments are fundamental to many sequence analysis methods. Most alignments are computed using the Progressive Alignment heuristic.  ...  In this paper, we describe a new program called Clustal Omega which can align virtually any number of protein sequences quickly and that delivers accurate alignments.  ...  The idea of EPA was suggested by KK. FS adapted HHalign to Clustal Omega; AW devised and adapted guide-tree construction routines. DD parallelised the code.  ... 
doi:10.1038/msb.2011.75 pmid:21988835 pmcid:PMC3261699 fatcat:bs7ngiylzjcdrefgzho3ni4dqy

Improving performance of multiple sequence alignment analysis in multi-client environments

U. Catalyurek, E. Stahlberg, R. Ferreira, T. Kurc, J. Saltz
2002 Proceedings 16th International Parallel and Distributed Processing Symposium  
This paper is concerned with the efficient execution of multiple sequence alignment methods in a multiple client environment.  ...  Our results also show that the cache-enabled CLUSTAL W program scales well on a SMP machine.  ...  Progressive Alignment: The last step is a constructive step, in which a series of pairwise alignments are computed using full dynamic programming to align larger and larger groups of sequences.  ... 
doi:10.1109/ipdps.2002.1016584 dblp:conf/ipps/CatalyurekSFKS02 fatcat:wq6keanlzrgubldxrkmgwf4iqy

POAVIZ: a Partial Order Multiple Sequence Alignment Visualizer

C. Grasso, M. Quist, K. Ke, C. Lee
2003 Bioinformatics  
POAVIZ creates a visualization of a multiple sequence alignment that makes clear the overall structure of how sequences match and diverge in the alignment.  ...  Alignment (POA) multiple sequence alignment program.  ...  For instance, running the POAVIZ program in conjunction with the Mathematica notebook on a 400 MHz Macintosh G4 to visualize a CLUSTAL formatted multiple sequence alignment containing 3 967 protein sequences  ... 
doi:10.1093/bioinformatics/btg175 pmid:12874062 fatcat:22tt2bs5qbhqjkmnnopeb2jlt4

SNAP: Combine and Map modules for multilocus population genetic analysis

D. L. Aylor, E. W. Price, I. Carbone
2006 Bioinformatics  
SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files.  ...  We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations.  ...  The conversion of combined PHYLIP files to CLUSTAL format is especially important when excluding strains from multiple alignments; this may result in suboptimal alignments with unnecessary alignment gaps  ... 
doi:10.1093/bioinformatics/btl136 pmid:16601003 fatcat:okrj3qwbifcbplm2ayecmbpeh4

Evolving Consensus Sequence for Multiple Sequence Alignment with a Genetic Algorithm [chapter]

Conrad Shyu, James A. Foster
2003 Lecture Notes in Computer Science  
In this paper we present an approach that evolves the consensus sequence [25] for multiple sequence alignment (MSA) with genetic algorithm (GA).  ...  We conducted some preliminary studies and compared our approach with the commonly used heuristic alignment program Clustal W. Results have shown that the GA can indeed scale and perform well. 2  ...  It builds up multiple alignments progressively with a series of pairwise alignments moving from the leaves upward in a guide tree that estimates the phylogeny of the sequences [9] .  ... 
doi:10.1007/3-540-45110-2_124 fatcat:bhz3zqaxkzh2bogl4m265kngeq

A hybrid genetic search for multiple sequence alignment

Seung-Hyun Moon, Sung-Soon Choi, Byung-Ro Moon
2006 Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06  
This paper proposes a hybrid genetic algorithm for multiple sequence alignment. The algorithm evolves guide sequences and aligns input sequences based on the guide sequences.  ...  In the experiments for various data sets, the proposed algorithm showed the performance comparable to existing algorithms.  ...  Each input sequence S is aligned so that S (S, G) is maximized by dynamic programming. The time complexity of the whole multiple alignment process is Θ(L 2 · N ).  ... 
doi:10.1145/1143997.1144051 dblp:conf/gecco/MoonCM06 fatcat:wtnd6rliqzaytepppfa3iz2b7i

FAMSA: Fast and accurate multiple sequence alignment of huge protein families

Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudyś
2016 Scientific Reports  
The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment algorithms.  ...  In the article we introduce FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences.  ...  Introduction The multiple sequence alignment (MSA) is one of the most important analyses in molecular biology.  ... 
doi:10.1038/srep33964 pmid:27670777 pmcid:PMC5037421 fatcat:5kwct7i2vrcq5bp4kvcyeafp6m

CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

Desmond G. Higgins, Paul M. Sharp
1988 Gene  
Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree.  ...  An approach for performing multiple alignments of large numbers of ammo acid or nucleotide sequences is described.  ...  ACKNOWLEDGEMENTS This is a publication from the Irish National Centre for Bioinformatics. This work was supported by grant No. BAP-0137~IRL from the European Community Biotechnology Action Programme.  ... 
doi:10.1016/0378-1119(88)90330-7 pmid:3243435 fatcat:g5fv47tgubacfm7kz4wmpzt4su
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