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,单击此处编辑母版标题样式,*,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,*,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,第六章 序列相似性搜索,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. 序列比较的任务：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,25%,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,。,1. 同源（homology）- 具有共同的祖先二、同源和相,三、序列的,BLAST,分析,三、序列的BLAST分析,BLAST (,B,asic,L,ocal,A,lignment,S,earch,T,ool) 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,BLAST (Basic Local Alignment S,Website of BLAST,http:/www.ncbi.nlm.nih.gov/BLAST/,(BLAST2.0),http:/www2.ebi.ac.uk/blast2/,(WU-Blast2),http:/blast.wustl.edu/,(WU-Blast2),Website of BLAST,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 proteins,discovering variants of genes or proteins,investigating expressed sequence tags (ESTs),exploring protein structure and function,Why use BLAST?BLAST searching,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 parameters,Then click “BLAST”,Four components to a BLAST sea,序列相似性搜索ppt课件,序列相似性搜索ppt课件,Step 1: Choose your sequence,Sequence can be input in FASTA format, plain text format or as accession number,Step 1: Choose your sequenceSe,Example of the FASTA format for a BLAST query,Example of the FASTA format fo,Step 2: Choose the BLAST program,Step 2: Choose the BLAST progr,Step 2: Choose the BLAST program,blastn (nucleotide BLAST),blastp (protein BLAST),blastx (translated BLAST),tblastn (translated BLAST),tblastx (translated BLAST),Step 2: Choose the BLAST progr,Choose the BLAST program,Program,Input,Database,1,blastn,DNA,DNA,1,blastp,protein,protein,6,blastx,DNA,protein,6,tblastn,protein,DNA,36,tblastx,DNA,DNA,Choose the BLAST programProgra,DNA potentially encodes six proteins,5 CAT CAA,5 ATC AAC,5 TCA ACT,5 GTG GGT,5 TGG GTA,5 GGG TAG,5 CATCAACTACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC 3,3 GTAGTTGATGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5,DNA potentially encodes six pr,Step 3: choose the database,nr = non-redundant (most general database),dbest = database of expressed sequence tags,dbsts = database of sequence tag sites,gss = genomic survey sequences,htgs = high throughput genomic sequence,Step 3: choose the database nr,Step 4a: Select optional search parameters,CD search,Step 4a: Select optional searc,BLAST N searching,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,Step 4a: Select optional searc,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 output format,BLAST: optional parameters You,filtering,filtering,序列相似性搜索ppt课件,序列相似性搜索ppt课件,Step 4b: optional formatting parameters,Alignment view,Descriptions,Alignments,Step 4b: optional formatting p,序列相似性搜索ppt课件,taxonomy,database,query,program,taxonomydatabasequeryprogram,taxonomy,taxonomy,序列相似性搜索ppt课件,序列相似性搜索ppt课件,BLAST format options,BLAST format options,BLAST format options: multiple sequence alignment,BLAST format options: multiple,序列相似性搜索ppt课件,threshold score = 11,EVD parameters,BLOSUM matrix,Effective search space,= mn,= length of query x db length,10.0 is the E value,gap penalties,cut-off parameters,We will get to the,bottom of a BLAST,search in a few,minutes,threshold score = 11EVD parame,BLASTP Searching with a multidomain protein, pol,BLASTP Searching with a multid,序列相似性搜索ppt课件,Searching bacterial sequences with pol,Searching bacterial sequences,BLAST program selection guide,BLAST program selection guide,Pig growth hormone mRNA,Sequence ID: gb|M22761.1|PIGGHMALength: 878Number of Matches:,Pig growth hormone mRNA,序列相似性搜索ppt课件,
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