教案4.生物信息学的基本概念与应用60.ppt

两条序列匹配比较III－终止 y=4 (1,-3,-2,-1) 延伸到第7个碱基的时候达到/超过了y的值，这时候延伸停止，返回去找得分最高的比对，结果就是ACGGT的比对，得分为5 两条序列匹配比较III－终止 X=4 (1,-3,-2,-1) 延伸到第7个碱基的时候达到/超过了X的值，这时候延伸停止，返回去找得分最高的比对，结果就是ACGGT的比对，得分为5 Dynamic Programing动态规划 Dynamic Programming允许最适比较，允许插入删除，全局，局部 Dynamic Programming allow Optimal Alignment between two sequences Allow Insertion and Deletion or Alignment with gaps Needlman and Wunsh Algorithm (1970) for global alignment Smith Waterman Algorithm (1981) for local alignment Important Steps Create DOTPLOT between two sequences散点图 Compute SUM matrix矩阵求和 Trace Optimal Path追踪最适途径 Steps for Dynamic Programming 。 Row gap Column gap Steps for Dynamic Programming Steps for Dynamic Programming Steps for Dynamic Programming BLAST中序列对库做比较 一条查询序列跟库中每条序列做两条序列的比较，把结果排序，得到了这条查询序列跟库中序列局部匹配比较好的结果 多条查询序列会被分解成单条序列与库中序列比较，得到一条一条查询序列结果的简单累积 BLAST类型 核酸－核酸 blastn 蛋白质－蛋白质 blastp 核酸T－蛋白质 blastx 蛋白质－核酸T tblastn 核酸T－核酸 T tblastx Traditional BLAST programs Program Database Query Typical uses BLASTN Nucleotide Nucleotide Mapping oligonucleotides, cDNAs, and PCR products to a genome; screening repetitive elements; cross-species sequence exploration; annotating genomic DNA; clustering sequencing reads; vector clipping BLASTP Protein Protein Identifying common regions between proteins; collecting related proteins for phylogenetic analyses BLASTX Protein Nucleotide translated into protein Finding protein-coding genes in genomic DNA; determining if a cDNA corresponds to a known protein TBLASTN Nucleotide translated into protein Protein Identifying transcripts, potentially from multiple organisms, similar to a given protein; mapping a protein to genomic DNA TBLASTX Nucleotide translated into protein Nucleotide translated into protein Cross-species gene prediction at the genome or transcript level; searching for genes missed by traditional methods or not yet in protein databases 生物信息学基础算法-BLAST BLAST主页 /BLAST/ 教程 /BLAST/tutorial/Altschul-1.html BLAST中的相似性分数的统计学意义/Education/B