Author pages are created from data sourced from our academic publisher partnerships and public sources.
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 pairwise… Expand
Recent developments in the MAFFT multiple sequence alignment program
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. Expand
Multiple alignment of DNA sequences with MAFFT.
We outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. Expand
Parallelization of the MAFFT multiple sequence alignment program
We parallelized the MAFFT MSA program using the POSIX Threads library for multiple sequence alignment. Expand
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
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
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 coupled… Expand
Improvement in the accuracy of multiple sequence alignment program MAFFT.
- K. Katoh, K. Kuma, T. Miyata, H. Toh
- Computer Science, Medicine
- Genome informatics. International Conference on…
We report a recent extension of MAFFT that aims to improve the accuracy with as little cost of calculation time as possible. Expand
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
We have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). Expand
A novel representation of protein sequences for prediction of subcellular location using support vector machines
- Setsuro Matsuda, Jean-Philippe Vert, Hiroto Saigo, N. Ueda, H. Toh, T. Akutsu
- Biology, Medicine
- Protein science : a publication of the Protein…
- 1 November 2005
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. In… Expand
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
- T. Sato, Yoshihiro Yamanishi, M. Kanehisa, H. Toh
- Biology, Computer Science
- 1 September 2005
We developed a novel method to predict protein-protein interactions from co-evolutionary information in the framework of the mirror tree method. Expand