IMPROVEMENTS AND EXTENSIONS TO THE BLAST ALGORITHMS

BLAST家族蛋白质和DNA数据库 搜索程序构成了提供的主要服务之一 NCBI.这些程序目前在NCBI服务器上运行， 在一个典型的工作日里有7万次。该项目代表了一个 不断努力改进和扩展这些系统的功能， rogrmas。本年度的进展包括：a） 改进的PSI-BLAST网页。此页面允许用户 选择或删除要包含在 PSI-BLAST位置特异性评分矩阵的构建 下次数据库搜索。该设施可以大大改善 搜索，以及随之而来的搜索敏感度的增加。新 网页还允许用户在多种氨基中进行选择 酸取代矩阵适合于不同程度的进化 发散此功能也已添加到标准中 BLAST页面。B）开发新程序PHI-BLAST， 用于使用模式作为种子来搜索蛋白质序列数据库。 蛋白质家族通常以保守序列为特征 图案或图案。研究人员经常希望评估 蛋白质内特定模式的重要性，或利用 已知图案的知识，以帮助识别大大 分歧但同源的家庭成员。协助这些 模式命中启动的BLAST（PHI-BLAST）程序 将蛋白质序列和感兴趣的模式两者作为输入， 它包含。PHI-BLAST在蛋白质数据库中搜索其他 实例，并将找到的实例用作 构建查询序列的局部比对。

The BLAST family of protein and DNA database search programs constitute one of the key services offered by the NCBI. These programs are currently run on NCBI servers about 70,000 times during a typical weekday. This project represents an ongoing effort to improve and extend the functionality of these rogrmas. Progress this year has included: a) The development of an improved PSI-BLAST web page. This page allows the user to select or deselect specific alignments for inclusion in the construction of the PSI-BLAST position-specific score matrix used for the next database search. This facility allows for greatly refined searches, and an attendant increase in search sensitivity. The new web page also permits the user to select among a variety of amino acid substitution matrices tailored to varyng degrees of evolutionary divergence. This feature has been added as well to the standard BLAST page. b) The development of a new program, PHI-BLAST, for searching protein sequence databases using patterns as seeds. Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the Pattern-Hit Initiated BLAST (PHI-BLAST) program takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence.