• Publications
  • Influence
MAFFT version 5: improvement in accuracy of multiple sequence alignment
The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwiseExpand
  • 3,933
  • 608
  • PDF
Recent developments in the MAFFT multiple sequence alignment program
  • K. Katoh, H. Toh
  • Biology, Computer Science
  • Briefings Bioinform.
  • 1 July 2008
TLDR
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. Expand
  • 2,964
  • 493
  • PDF
Multiple alignment of DNA sequences with MAFFT.
TLDR
We outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. Expand
  • 1,027
  • 141
Parallelization of the MAFFT multiple sequence alignment program
TLDR
We parallelized the MAFFT MSA program using the POSIX Threads library for multiple sequence alignment. Expand
  • 592
  • 86
  • PDF
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
  • K. Katoh, H. Toh
  • Biology, Computer Science
  • BMC Bioinformatics
  • 25 April 2008
TLDR
We developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Expand
  • 479
  • 69
  • PDF
Identification of a new cryptochrome class. Structure, function, and evolution.
Cryptochrome flavoproteins, which share sequence homology with light-dependent DNA repair photolyases, function as photoreceptors in plants and circadian clock components in animals. Here, we coupledExpand
  • 283
  • 24
Improvement in the accuracy of multiple sequence alignment program MAFFT.
TLDR
We report a recent extension of MAFFT that aims to improve the accuracy with as little cost of calculation time as possible. Expand
  • 141
  • 21
  • PDF
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
TLDR
We have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). Expand
  • 103
  • 16
  • PDF
A novel representation of protein sequences for prediction of subcellular location using support vector machines
As the number of complete genomes rapidly increases, accurate methods to automatically predict the subcellular location of proteins are increasingly useful to help their functional annotation. InExpand
  • 151
  • 15
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
TLDR
We developed a novel method to predict protein-protein interactions from co-evolutionary information in the framework of the mirror tree method. Expand
  • 132
  • 14
  • PDF
...
1
2
3
4
5
...