Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
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DOI：
10.1093/bioinformatics/bth126
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发表时间：
2004-07-01
期刊：
影响因子：
5.8
通讯作者：
Lee, C
中科院分区：
文献类型：
--
作者：
Grasso, C;Lee, C
动机：偏序比对(POA)被提出为多序列比对(MSA)的一种新方法，它可以与现有的方法相结合，如渐进比对。这对于解决POA原始版本中存在的问题(如阶数敏感性)和标准渐进比对程序中的问题(如复杂比对中的信息丢失，特别是周围间隙区域的信息丢失)具有重要意义。结果：我们提出了一种新的偏序-偏序比对算法，该算法对一对MSA进行最优比对，因此可以直接应用于CLUSTAL等渐进比对方法。使用该算法，我们表明，组合渐进POA比对方法产生的结果与最好的可用的MSA程序(CLUSTALW，DIALIGN2，T-CAFEE)相当，但速度要快得多。例如，根据序列相似性的水平，在标准PC上比对1000个序列，每个500个氨基酸长，花费15分钟(平均同源性为90%)到44分钟(同源性为30%)。对于大比对，渐进POA的速度是之前三种方法中最快的(CLUSTALW)的10-30倍。这些数据表明，与以前的方法相比，基于POA的方法可以解决更大的比对问题。
Motivation: Partial order alignment (POA) has been proposed as a new approach to multiple sequence alignment (MSA), which can be combined with existing methods such as progressive alignment. This is important for addressing problems both in the original version of POA (such as order sensitivity) and in standard progressive alignment programs (such as information loss in complex alignments, especially surrounding gap regions).Results: We have developed a new Partial Order-Partial Order alignment algorithm that optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. Using this algorithm, we show the combined Progressive POA alignment method yields results comparable with the best available MSA programs (CLUSTALW, DIALIGN2, T-COFFEE) but is far faster. For example, depending on the level of sequence similarity, aligning 1000 sequences, each 500 amino acids long, took 15 min (at 90% average identity) to 44 min (at 30% identity) on a standard PC. For large alignments, Progressive POA was 10-30 times faster than the fastest of the three previous methods (CLUSTALW). These data suggest that POA-based methods can scale to much larger alignment problems than possible for previous methods.