IMPROVED SENSITIVITY OF NUCLEIC ACID DATABASE SEARCHES USING APPLICATION-SPECIFIC SCORING MATRICES
IMPROVED SENSITIVITY OF NUCLEIC ACID DATABASE SEARCHES USING APPLICATION-SPECIFIC SCORING MATRICES
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DOI：
10.1016/s1046-2023(05)80165-3
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发表时间：
1991-01-01
期刊：
影响因子：
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通讯作者：
ALTSCHUL S F
中科院分区：
文献类型：
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作者：
STATES D J;GISH W;ALTSCHUL S F
给出了基于适于分析分子测序错误或生物突变过程的模型的核酸序列比较的评分矩阵。在哺乳动物基因组中，转换突变发生的频率明显高于颠换，基于这种替代模型的序列比对的最佳评分不同于假设统一突变模型得出的评分。将使用最佳评分系统可能获得的序列比对信息与使用BLACKS默认评分获得的信息进行比较。改进的BLAST数据库搜索工具允许这些或其他明确指定的评分矩阵用于具有核酸查询序列的核酸数据库的计算有效查询。使用BLACKS的默认评分矩阵进行搜索的结果进行比较，与那些使用的分数的基础上的突变模型，其中转换比颠换更普遍。
Scoring matrices for nucleic acid sequence comparison that are based on models appropriate to the analysis of molecular sequencing errors or biological mutation processes are presented. In mammalian genomes, transition mutations occur significantly more frequently than transversions, and the optimal scoring of sequence alignments based on this substitution model differs from that derived assuming a uniform mutation model. The information from sequence alignments potentially available using an optimal scoring system is compared with that obtained using the BLASTN default scoring. A modified BLAST database search tool allows these, or other explicitly specified scoring matrices, to be utilized in computationally efficient queries of nucleic acid databases with nucleic acid query sequences. Results of searches performed using BLASTN's default score matrix are compared with those using scores based on a mutational model in which transitions are more prevalent than transversions.