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Journal Article•DOI•

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Kazutaka Katoh1, Kazuharu Misawa, Kei-ichi Kuma1, Takashi Miyata1•
Kyoto University1
15 Jul 2002-Nucleic Acids Research (Oxford University Press)-Vol. 30, Iss: 14, pp 3059-3066
TL;DR: A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Abstract: A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

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Citations
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Journal Article•DOI•
MUSCLE: multiple sequence alignment with high accuracy and high throughput

[...]

Robert C. Edgar
01 Mar 2004-Nucleic Acids Research
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Abstract: We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using treedependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

37,524 citations

Cites background or methods from "MAFFT: a novel method for rapid mul..."

  • ...for alignment accuracy discrimination (5,7,8) as fewer assumptions are made about the population distribution....

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  • ...Positionspeci®c gap penalties are used, employing heuristics similar to those found in MAFFT and LAGAN (17)....

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  • ...This is similar to the strategies used by PRRP (7) and MAFFT (8)....

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  • ...Tested versions were MUSCLE 3.2, CLUSTALW 1.82, T-Coffee 1.37 and MAFFT 3.82....

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  • ...We compared these with four other methods: CLUSTALW (25), probably the most widely used program at the time of writing; T-Coffee, which has the best BAliBASE score reported to date; and two MAFFT scripts: FFTNS1, the fastest previously published method known to the author (in which diagonal ®nding by fast Fourier transform is enabled and a progressive alignment constructed), and NWNSI, the slowest but most accurate of the MAFFT methods (in which fast Fourier transform is disabled and re®nement is enabled)....

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Journal Article•DOI•
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

[...]

Kazutaka Katoh1, Daron M. Standley1•
Osaka University1
01 Apr 2013-Molecular Biology and Evolution
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

27,771 citations

Cites methods from "MAFFT: a novel method for rapid mul..."

  • ...MAFFT is an MSA program, first released in 2002 (Katoh et al. 2002)....

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Journal Article•DOI•
Clustal W and Clustal X version 2.0

[...]

Mark A. Larkin1, Gordon Blackshields2, Nigel P. Brown2, R. Chenna2, Paul A. McGettigan2, Hamish McWilliam2, Franck Valentin2, Iain M. Wallace2, Andreas Wilm2, Rodrigo Lopez2, J.D. Thompson2, Toby J. Gibson2, Desmond G. Higgins2 •
University College Dublin1, European Bioinformatics Institute2
01 Nov 2007-Bioinformatics
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Abstract: Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact: clustalw@ucd.ie

25,325 citations

Cites background from "MAFFT: a novel method for rapid mul..."

  • ...Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2....

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Journal Article•DOI•
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

[...]

Fabian Sievers1, Andreas Wilm2, David Dineen1, Toby J. Gibson, Kevin Karplus3, Weizhong Li4, Rodrigo Lopez4, Hamish McWilliam4, Michael Remmert5, Johannes Söding5, Julie D. Thompson6, Desmond G. Higgins1 •
University College Dublin1, Genome Institute of Singapore2, University of California, Santa Cruz3, European Bioinformatics Institute4, Ludwig Maximilian University of Munich5, University of Strasbourg6
01 Jan 2011-Molecular Systems Biology
TL;DR: A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Abstract: Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. 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 accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

12,489 citations

Cites background from "MAFFT: a novel method for rapid mul..."

  • ...1 (http://www.clustal.org) DIALIGN 2.2.1 (http://dialign.gobics.de/) FSA 1.15.5 (http://sourceforge.net/projects/fsa/) Kalign 2.04 (http://msa.sbc.su.se/cgi-bin/msa.cgi) MAFFT 6.857 (http://mafft.cbrc.jp/alignment/software/source.html) MSAProbs 0.9.4 (http://sourceforge.net/projects/msaprobs/files/) MUSCLE version 3.8.31 posted 1 May 2010 (http://www.drive5. com/muscle/downloads.htm) PRANKv.100802, 2August 2010 (http://www.ebi.ac.uk/goldman-srv/ prank/src/prank/) Probalign v1....

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  • ...The consistency-based programsMSAprobs,MAFFT L-INS-i, Probalign, Probcons and T-Coffee, are again the most accurate but with long run times....

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  • ...For these tests, we just report results using the default settings for all programs but with two exceptions, which were needed to allow MUSCLE (Edgar, 2004) and MAFFT to align the biggest test cases in HomFam....

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  • ...There is then a gap to the faster progressive based programs of MUSCLE, MAFFT, Kalign (Lassmann and Sonnhammer, 2005) and Clustal W. Results from testing large alignments with up to 50000 sequences are given in Table III using HomFam....

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  • ...MAFFT with default settings, has a limit of 20000 sequences and we only use MAFFT with –parttree for the last section of Table III....

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Journal Article•DOI•
Database resources of the National Center for Biotechnology Information

[...]

David L. Wheeler1, Deanna M. Church1, Ron Edgar1, Scott Federhen1, Wolfgang Helmberg1, Thomas L. Madden1, Joan Pontius1, Gregory D. Schuler1, Lynn M. Schriml1, Edwin Sequeira1, Tugba O. Suzek1, Tatiana Tatusova1, Lukas Wagner1 •
National Institutes of Health1
01 Jan 2004-Nucleic Acids Research
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Abstract: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

9,604 citations

References
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Journal Article•DOI•
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

[...]

Stephen F. Altschul1, Thomas L. Madden, Alejandro A. Schäffer1, Jinghui Zhang, Zheng Zhang2, Webb Miller2, David J. Lipman •
National Institutes of Health1, Pennsylvania State University2
01 Sep 1997-Nucleic Acids Research
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

70,111 citations

"MAFFT: a novel method for rapid mul..." refers methods in this paper

  • ...There are well-known homology search programs, such as FASTA (11) and BLAST (12), based on string matching algorithms....

    [...]

Journal Article•DOI•
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
11 Nov 1994-Nucleic Acids Research
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

63,427 citations

"MAFFT: a novel method for rapid mul..." refers background or methods or result in this paper

  • ...AP-2, NW-NS-2, FFT-NS-2 and FFT-NS-i, to this database to compare their efficiencies with those of five existing methods, DIALIGN (29,30), PIMA (31), CLUSTALW ( 7 ) version 1.82, PRRP (32) and T-COFFEE (9)....

    [...]

  • ...Considerable improvements in the accuracy have recently been made in CLUSTALW ( 7 ) version 1.8, the most popular alignment program with excellent portability and operativity, and T-COFFEE (9), which provides alignments of the highest accuracy among known methods to date....

    [...]

  • ...Gotoh (6) and Thompson et al. ( 7 ) developed position-specific gap penalties depending on the pattern of existing gaps....

    [...]

  • ...where wi is the weighting factor for sequence i, which is calculated in the same manner as CLUSTALW ( 7 ) for the progressive method, or in the same manner as Gotoh’s (20) weighting system for the iterative refinement method....

    [...]

  • ...Thompson et al. ( 7 ) developed a complicated scoring system in their program CLUSTALW, in which gap penalties and other parameters are carefully adjusted according to the features of input sequences, such as sequence divergence, length, local hydropathy and so on. Nevertheless, no existing scoring system is able to process correctly global alignments for various types of problems including large terminal extension of internal insertion (8)....

    [...]

Journal Article•DOI•
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

[...]

Motoo Kimura1•
National Institute of Genetics1
01 Dec 1980-Journal of Molecular Evolution
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

26,016 citations

Book•
Numerical Recipes in C: The Art of Scientific Computing

[...]

William H. Press1, Brian P. Flannery2, Saul A. Teukolsky3, William T. Vetterling4•
Harvard University1, ExxonMobil2, Cornell University3, Polaroid Corporation4
31 Jan 1986
TL;DR: Numerical Recipes: The Art of Scientific Computing as discussed by the authors is a complete text and reference book on scientific computing with over 100 new routines (now well over 300 in all), plus upgraded versions of many of the original routines, with many new topics presented at the same accessible level.
Abstract: From the Publisher: This is the revised and greatly expanded Second Edition of the hugely popular Numerical Recipes: The Art of Scientific Computing. The product of a unique collaboration among four leading scientists in academic research and industry, Numerical Recipes is a complete text and reference book on scientific computing. In a self-contained manner it proceeds from mathematical and theoretical considerations to actual practical computer routines. With over 100 new routines (now well over 300 in all), plus upgraded versions of many of the original routines, this book is more than ever the most practical, comprehensive handbook of scientific computing available today. The book retains the informal, easy-to-read style that made the first edition so popular, with many new topics presented at the same accessible level. In addition, some sections of more advanced material have been introduced, set off in small type from the main body of the text. Numerical Recipes is an ideal textbook for scientists and engineers and an indispensable reference for anyone who works in scientific computing. Highlights of the new material include a new chapter on integral equations and inverse methods; multigrid methods for solving partial differential equations; improved random number routines; wavelet transforms; the statistical bootstrap method; a new chapter on "less-numerical" algorithms including compression coding and arbitrary precision arithmetic; band diagonal linear systems; linear algebra on sparse matrices; Cholesky and QR decomposition; calculation of numerical derivatives; Pade approximants, and rational Chebyshev approximation; new special functions; Monte Carlo integration in high-dimensional spaces; globally convergent methods for sets of nonlinear equations; an expanded chapter on fast Fourier methods; spectral analysis on unevenly sampled data; Savitzky-Golay smoothing filters; and two-dimensional Kolmogorov-Smirnoff tests. All this is in addition to material on such basic top

12,662 citations

Journal Article•DOI•
Improved tools for biological sequence comparison.

[...]

William R. Pearson1, David J. Lipman•
University of Virginia1
01 Apr 1988-Proceedings of the National Academy of Sciences of the United States of America
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
Abstract: We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.

12,432 citations

"MAFFT: a novel method for rapid mul..." refers methods in this paper

  • ...There are well-known homology search programs, such as FASTA (11) and BLAST (12), based on string matching algorithms....

    [...]

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