Improvements and Extensions to the BLAST Algorithms

今年该项目的一个持续重点是调查 提高Delta-BLAST检索精度的途径探讨 使用“模型手术”和不对称但统一的缺口成本。 传统上，PSI-BLAST构建其特定于位置的分数 矩阵(PSSM)使用查询序列作为模板，每个 氨基酸作为基质的一列的占位符。 然而，如果查询序列包括非典型插入 或删除，则产生的PSSM将在具有 在对齐时暗示相应的删除或插入 最相关的序列。最近开发的Delta-BLAST 首先将查询序列与PSSM数据库进行比对，这 打开允许构造的PSSM获取 它的长度来自任何对齐的PSSM，而不是来自查询。 此外，还可以处理插入和删除 关于使用这种模型手术构建的PSSM 不对称的，例如，惩罚插入小于 删除。我们在统计上取得了显著的进步 使用这种方法。 关于BLAST算法和程序的最新文章是 为《生命科学百科全书》写的。

A continuing focus of the project this year was the investigation of ways to improve the retrieval accuracy of DELTA-BLAST through the use of "model surgery" and of asymmetric but uniform gap costs. Traditionally, PSI-BLAST constructs its position specific score matrix (PSSM) using the query sequence as a template, with each amino acid serving as a place holder for a column of the matrix. However, if the query sequence includes an atypical insertion or deletion, the resulting PSSM will be handicapped in having to imply a corresponding deletion or insertion when aligning to most related sequences. The recently developed DELTA-BLAST first aligns a query sequence to a database of PSSMs, and this opens the possibility of allowing the constucted PSSM to take its length from any aligned PSSMs rather than from the query. Furthermore, it is possible to treat insertions and deletions with respect to PSSMs constructed using such model surgery asymmetrically, for example penalizing insertions less than deletions. We achieved statistically significant improvements using this approach. An updated article on the BLAST algorithm and programs was written for the Encyclopedia of Life Sciences.