Statistics Of Sequence Comparison

今年的工作重点是分析各种影响， 在检索的间隙成本规范的变化 蛋白质图谱搜索算法的准确性， 提高PSI-BLAST的检索精度。 简而言之，引入特定位置替换 大大提高了蛋白质测序的灵敏度 数据库搜索程序：PSI-BLAST和相关的隐马尔可夫 模型（HMM）程序能够识别更远的距离 序列关系比BLAST更好。 HMM程序可以采用 具体的差距成本也。 通过修改这些程序， 我们发现， 考虑了插入的特定氨基酸， 的页面不存在或 然而，我们发现， 差距成本因其位置而异。 将位置特异性空位成本并入PSI-BLAST需要 准确描述其使用的PSI-BLAST统计数据。 实现这一目标的最有希望的途径是调整 与PSI-BLAST一起使用的杂交比对评分方法。

Work this year focused on an analysis of the effects of various changes in the specification of gap costs on the retrieval accuracy of protein profile search algorithms, with a view towards improving the retrieval accuracy of PSI-BLAST. In brief, the introduction of position-specific substitution costs has greatly improved the sensitivity of protein sequence database search programs: PSI-BLAST and related Hidden Markov Model (HMM) programs are able to recognize much more distant sequence relationships than can BLAST. HMM programs may employ position-specific gap costs as well. By modifying these programs, we found no improvement from position-specific gap costs that took account of the specific amino acids that were inserted or deleted. However, we did find a significant improvement from gap costs that varied according to their location. Incorporating position-specific gap costs into PSI-BLAST requires an accurate description of PSI-BLAST statistics under their use. The most promising path to this goal is the adaptation of the hybrid alignment scoring method for use with PSI-BLAST.