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
Hepatitis E virus genotype 3 in wild rats, United States.
TL;DR: Rodents infected with this virus may be a serious threat to public health and may need to be removed.
Journal ArticleDOI
Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche.
Paul-Adrian Bulzu,Adrian-Ştefan Andrei,Michaela M. Salcher,Michaela M. Salcher,Maliheh Mehrshad,Keiichi Inoue,Hideki Kandori,Oded Béjà,Rohit Ghai,Horia L. Banciu +9 more
TL;DR: A comparative analysis of Asgard archaea genomes elucidates their metabolic potential and leads to the proposal of a revised ‘aerobic protoeukaryotes’ model for the origin of the eukaryotic cell.
Journal ArticleDOI
Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins
TL;DR: A model of TMC1 is generated based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway.
Journal ArticleDOI
Comparative genomics reveals the origin of fungal hyphae and multicellularity.
Enikő Csilla Kiss,Botond Hegedis,Máté Virágh,Torda Varga,Zsolt Merényi,Tamás Kószó,Balázs Bálint,Arun N. Prasanna,Krisztina Krizsán,Sándor Kocsubé,Meritxell Riquelme,Norio Takeshita,László Nagy +12 more
TL;DR: It is shown that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic genes, the origin of new gene families, gene duplications and alterations of gene structure, among others.
Journal ArticleDOI
Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes)
TL;DR: The study confirmed, based on a larger dataset than previous work, that the anther smuts on Caryophyllaceae are monophyletic and that there exists a native North American group that diverged from the European clade before the radiation of the European species.
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.