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1、第六章 序列相似性搜索,一、序列相似性搜索的任务和目的序列相似性搜索的任务序列相似性搜索的目的二、同源和相似三、序列的BLAST分析四、专门的BLAST服务器,1.序列比较的任务：发现序列之间的相似性辨别序列之间的差异2.目的：相似序列 相似的结构，相似的功能 判别序列之间的同源性 推测序列之间的进化关系,一、序列相似性搜索的任务和目的,1.同源（homology）-具有共同的祖先 直向同源（Orthologous）共生同源（paralogous）2.相似（similarity）同源序列一般是相似的 相似序列不一定是同源的,二、同源和相似,一般认为，蛋白质序列间至少有80个氨基酸左右的区域有2
2、5%或更高的同源性；DNA序列具有75%以上的同源性有潜在的生物学意义。,三、序列的BLAST分析,BLAST(Basic Local Alignment Search Tool)allows rapid sequence comparison of a query sequence against a database.The BLAST algorithm is fast,accurate,and web-accessible.基本局域联配搜寻工具,BLAST,Website of BLASThttp:/www.ncbi.nlm.nih.gov/BLAST/(BLAST2.0)http:/
3、www2.ebi.ac.uk/blast2/(WU-Blast2)http:/blast.wustl.edu/(WU-Blast2),Why use BLAST?,BLAST searching is fundamental to understanding the relatedness of any favorite query sequence to other known proteins or DNA sequences.Applications include identifying orthologs and paralogs discovering new genes or p
4、roteins discovering variants of genes or proteins investigating expressed sequence tags(ESTs)exploring protein structure and function,Four components to a BLAST search,(1)Choose the sequence(query)(2)Select the BLAST program(3)Choose the database to search(4)Choose optional parametersThen click“BLAS
5、T”,Step 1:Choose your sequence,Sequence can be input in FASTA format,plain text format or as accession number,Example of the FASTA format for a BLAST query,Step 2:Choose the BLAST program,Step 2:Choose the BLAST program,blastn(nucleotide BLAST)blastp(protein BLAST)blastx(translated BLAST)tblastn(tra
6、nslated BLAST)tblastx(translated BLAST),Choose the BLAST program,ProgramInputDatabase 1blastnDNADNA 1blastpproteinprotein 6blastxDNAprotein 6tblastnprotein DNA 36tblastxDNA DNA,DNA potentially encodes six proteins,5 CAT CAA 5 ATC AAC 5 TCA ACT,5 GTG GGT 5 TGG GTA 5 GGG TAG,5 CATCAACTACAACTCCAAAGACAC
7、CCTTACACATCAACAAACCTACCCAC 33 GTAGTTGATGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5,Step 3:choose the database,nr=non-redundant(most general database)dbest=database of expressed sequence tagsdbsts=database of sequence tag sitesgss=genomic survey sequenceshtgs=high throughput genomic sequence,Step 4a:
8、Select optional search parameters,CD search,BLAST N searching,Step 4a:Select optional search parameters,Entrez!,Filter,Expect,Word size,organism,增加该值可提高查询速度,BLAST:optional parameters,You can.choose the organism to search turn filtering on/off change the expect(e)value change the word size change the
9、 output format,filtering,Step 4b:optional formatting parameters,Alignment viewDescriptionsAlignments,taxonomy,database,query,program,taxonomy,BLAST format options,BLAST format options:multiple sequence alignment,threshold score=11,EVD parameters,BLOSUM matrix,Effective search space=mn=length of quer
10、y x db length,10.0 is the E value,gap penalties,cut-off parameters,We will get to thebottom of a BLASTsearch in a fewminutes,BLASTP Searching with a multidomain protein,pol,Searching bacterial sequences with pol,BLAST program selection guide,Pig growth hormone mRNASequence ID:gb|M22761.1|PIGGHMALength:878Number of Matches:,
