MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Reads0
Chats0
TLDR
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.read more
Citations
More filters
Journal ArticleDOI
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
TL;DR: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.
Journal ArticleDOI
MAFFT version 5: improvement in accuracy of multiple sequence alignment
TL;DR: Improvement in accuracy was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here, which showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences.
Journal ArticleDOI
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
Gerard Talavera,Jose Castresana +1 more
TL;DR: Whether phylogenetic reconstruction improves after alignment cleaning or not is examined and cleaned alignments produce better topologies although, paradoxically, with lower bootstrap, which indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
Journal ArticleDOI
MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization
TL;DR: The Web interface for recently developed options for large data and interactive usage to refine sequence data sets and MSAs for multiple sequence alignment are explained.
Journal ArticleDOI
Recent developments in the MAFFT multiple sequence alignment program
Kazutaka Katoh,Hiroyuki Toh +1 more
TL;DR: The initial version of the MAFFT program was developed in 2002 and was updated in 2007 with two new techniques: the PartTree algorithm and the Four-way consistency objective function, which improved the scalability of progressive alignment and the accuracy of ncRNA alignment.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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.
Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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.
Journal ArticleDOI
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
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.
Book
Numerical Recipes in C: The Art of Scientific Computing
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.
Journal ArticleDOI
Improved tools for biological sequence comparison.
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.