MAFFT version 5: improvement in accuracy of multiple sequence alignment.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
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DOI：
10.1093/nar/gki198
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发表时间：
2005
影响因子：
14.9
通讯作者：
Miyata T
中科院分区：
文献类型：
--
作者：
Katoh K;Kuma K;Toh H;Miyata T
多个序列对齐程序MAFFT的准确性已得到改善。合并到目标功能中。 > 50个序列。相似性较低，将序列与收集的数十个近距离同源物（E-Value <10-5-10-20）对齐时提高了精度（2-10个百分点）从数据库中，对于大多数方法都可以观察到这种改进，但在这里提出的新选择非常大，我们制作了一个Ruby脚本Maffte.rb使用NCBI-Blast。
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 alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of ∼8 sequences with low similarity, the accuracy was improved (2–10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10−5–10−20) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
3.9
作者：
Tateno, Y;Ikeo, K;Gojobori, T
通讯作者：
Gojobori, T
影响因子：
14.9
作者：
Thompson, JD;Plewniak, F;Poch, O
通讯作者：
Poch, O
影响因子：
5.6
作者：
Gotoh, O
通讯作者：
Gotoh, O
DOI：
10.1073/pnas.85.8.2444
发表时间：
1988-04-01
影响因子：
11.1
作者：
PEARSON, WR;LIPMAN, DJ
通讯作者：
LIPMAN, DJ