Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
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DOI：
10.1093/nar/gkn1006
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发表时间：
2009-02
影响因子：
14.9
通讯作者：
Sonnhammer EL
中科院分区：
文献类型：
--
作者：
Lassmann T;Frings O;Sonnhammer EL
在不断发展的基因组学领域，多个比对程序面临着不断增加的数据量。为了解决这个日益严重的问题，我们极大地改进了Kalign的运行时间和内存需求，同时保持其高对齐精度。Kalign version 2还支持核苷酸比对，并且新引入的扩展允许将外部序列注释包含到比对过程中。我们证明了Kalign2是非常快速和内存高效的，允许非常大量的序列的精确对齐。Kalign2的准确性与蛋白质比对的最佳方法相比要好，而其对核苷酸比对的准确性通常更优越。此外，我们还展示了使用已知或预测序列注释来提高比对精度的潜力。Kalign2可以从Kalign网站（http://msa.sbc.su.se/）免费下载。
In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
5.8
作者：
Stoye, J;Evers, D;Meyer, F
通讯作者：
Meyer, F
影响因子：
3
作者：
Thompson JD;Muller A;Waterhouse A;Procter J;Barton GJ;Plewniak F;Poch O
通讯作者：
Poch O
影响因子：
3
作者：
Lassmann T;Sonnhammer EL
通讯作者：
Sonnhammer EL