Parallelization of the MAFFT multiple sequence alignment program
نویسندگان
چکیده
منابع مشابه
Parallelization of the MAFFT multiple sequence alignment program
SUMMARY Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural paralleliz...
متن کاملImprovement in the accuracy of multiple sequence alignment program MAFFT.
In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, bot...
متن کاملRecent 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. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence dat...
متن کاملA simple method to control over-alignment in the MAFFT multiple sequence alignment program
MOTIVATION We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequenci...
متن کاملParallelization of MAFFT for large-scale multiple sequence alignments.
Summary We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most largescale analyses, due to the requirement of large computational resources. We introduce a scalable ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2010
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btq224