New finite-size correction for local alignment score distributions.
New finite-size correction for local alignment score distributions.
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DOI：
10.1186/1756-0500-5-286
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发表时间：
2012-06-12
影响因子：
1.8
通讯作者：
Spouge JL
中科院分区：
文献类型：
--
作者：
Park Y;Sheetlin S;Ma N;Madden TL;Spouge JL
局部比对程序经常计算偶然匹配的概率。该概率的计算可能需要对序列的长度进行“有限大小”校正，因为在任一序列的末端附近开始的比对可能在达到显著分数之前用完序列。我们提出了一种改进的有限大小的校正，考虑序列长度的分布，而不是简单的相应的手段。这种方法提高了灵敏度，并避免了用临时长度替代可能低估匹配重要性的短序列。我们使用来自ASTRAL的测试集来显示改进的ROC分数，特别是对于较短的序列。新的有限尺寸校正改进了局部比对的概率计算。它现在用于BLAST+包和NCBI BLAST网站（http://blast.ncbi.nlm.nih.gov）。
Local alignment programs often calculate the probability that a match occurred by chance. The calculation of this probability may require a “finite-size” correction to the lengths of the sequences, as an alignment that starts near the end of either sequence may run out of sequence before achieving a significant score. We present an improved finite-size correction that considers the distribution of sequence lengths rather than simply the corresponding means. This approach improves sensitivity and avoids substituting an ad hoc length for short sequences that can underestimate the significance of a match. We use a test set derived from ASTRAL to show improved ROC scores, especially for shorter sequences. The new finite-size correction improves the calculation of probabilities for a local alignment. It is now used in the BLAST+ package and at the NCBI BLAST web site ( http://blast.ncbi.nlm.nih.gov).