根据多条序列比对结果计算信息含量的P值。
Computing the P-value of the information content from an alignment of multiple sequences.
作者信息
Nagarajan Niranjan, Jones Neil, Keich Uri
机构信息
Computer Science Department 4130 Upson Hall Cornell University Ithaca, NY 14853, USA.
出版信息
Bioinformatics. 2005 Jun;21 Suppl 1:i311-8. doi: 10.1093/bioinformatics/bti1044.
MOTIVATION
The efficient and accurate computation of P-values is an essential requirement for motif-finding and alignment tools. We show that the approximation algorithms used in two popular motif-finding programs, MEME and Consensus, can fail to accurately compute the P-value.
RESULTS
We present two new algorithms: one for the evaluation of the P-values of a range of motif scores, and a faster one for the evaluation of the P-value of a single motif score. Both exhibit more reliability than existing algorithms, and the latter algorithm is comparable in speed to the fastest existing method.
AVAILABILITY
The algorithms described in this paper are available from http://www.cs.cornell.edu/~keich
动机
P值的高效准确计算是基序查找和比对工具的一项基本要求。我们表明，两个流行的基序查找程序MEME和Consensus中使用的近似算法可能无法准确计算P值。
结果
我们提出了两种新算法：一种用于评估一系列基序得分的P值，另一种用于评估单个基序得分的P值的更快算法。两者都比现有算法表现出更高的可靠性，并且后一种算法在速度上与现有的最快方法相当。
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