A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Multiple sequence alignment with the Clustal series of programs
2003
Nucleic Acids Research
Preserved Fulltext
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
1998
TIBS -Trends in Biochemical Sciences. Regular ed
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
1994
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
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
1997
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2007; you can also visit the original URL.
The file type is application/pdf.
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
2014
Algorithms for Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2002
Genome Informatics Series
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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]
2002
Methods of biochemical analysis
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
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
2014
Molecular Systems Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2002
Proceedings 16th International Parallel and Distributed Processing Symposium
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2003
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2004; you can also visit the original URL.
The file type is application/pdf.
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
2006
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2003
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2006
Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Note that this fulltext copy is not of the "primary" version of this work. The version it corresponds to is:
2016 pre-print arXiv:1603.06958v1 fatcat:g7akab26cjagvcrjtqkxwjwhca
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
1988
Gene
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 8,379 results