10 - PCR引物设计(一)汇总

1第4章生物信息学应用软件4.1DNAStar4.2DNAMAN4.3GeneDoc24.1DNAStarDNAStar的主要功能：EditSeq序列编辑GeneQuest基因搜索MapDraw图谱绘制MegAlign序列比对PrimerSelect引物设计Protean蛋白分析SeqManII序列组装3安装DNAStar应用软件从“Bioinformatics→Programs”文件夹中找Dnastar可执行文件，双击启动安装，安装完成后从“开始”→“程序”中点击“DNAstar”，选择所需程序运行。44.1.1EditSeqClickhere.开始→程序→DNAStar→EditSeq5Example4-1试对下面的DNA序列进行EditSeq分析.ggcacgaggcgacgaaacaatacttgcctgatttaaacgattataagttttgttaaggaaaaactgtgatcagcttcaaattattttcaaattccgcgtaatctccaagatgtcacacaatggaactttggatgaacattatcagaccgtgagggaattttacgatggtaaatccgtttttattacaggagcgaccggattccttggaaaggcgtacgttgagaaacttgcgtattcgtgtccgggcatagtaagcatttacattttgattcgagacaagaaagggtcgaacactgaagagcgaatgagaaaatatcttgatcagcccattttttcacgaataaaatacgaacatccagaatatttcaaaaaaatcattcccatctctggtgatatcaccgcacccaaactaggattgtgcgatgaagaaagaaatatattaatcaacgaggtgtcgatagtgattcactcagccgcttcggtcaaactaaacgatcatttaaaatttactctgaacacgaatgttggaggtacgatgaaagtgttggaactcgttaaagaaatgaaaaacttagcgatgttcgtatatgtgtctacagcttattctaacacaagtcaaagaattttagaagaaaaactttatcctcagtccctaaatctaaacgaaatacagaagttcgctgaagaacattatatattaggtaaagacaacgatgaaatgataaaatttataggtaaccacccaaacacatatgcatacacaaaagcgctggcagaaaacttagttgctgaagaacacggtgaaataccaacaattatcattaggccttcgattattacagcgagtgctgaagagccagtgcgagggttcgtggatagttggagtggtgcaactgctatggcagcatttgctttgaagggatggaacaacataatgtacagcacaggcgaggagaatattgatctgatacctctagactatgttgtcaaccttacattagtagcgattgctaaatataagcctaccaaagaggtcacagtatatcacgtcacaaccagcgatcttaatcccatttcaatccgaagaatatttataaagctctccgaattcgcatcaaaaaatccaacgagtaatgccgcaccattcgcagcaacgactttattgactaaacagaagccattaataaaactggtcacgtttctcatgcagaccacgccggctttcctagctgacttatggatgaaaacccagaggaaagaagccaaattcgtcaagcaacataatctagtagtgagaagtcgtgatcaactggaattcttcacgtctcagtcgtggttgcttcgttgcgagcgagcccgtgtgcttagtgcggcactgagcgattcagaccgcgctgtcttccgctgcgatccttccaccatagactgggaccaatatttgccaatatacttcgaaggaatcaacaagcatctgttcaaaaataaattatagtcgattcctaataggcttgtaattgattccaaaaatacttagataacaataactttaatcaactacaatgaaataaatgtaaagtcgtcgtgacctataggataagacgtacggtgcattcgtatatagcgatgcaccggtgttcgaatcccgcaggcggataccaatttttctaatgaaatacgtacttaacaaatgttcacgattgacttccgcggtgaaggaacaacatcgtgtaataaaaatcaaacccgcaaaattataatttgcgtaattactggtggtaggacctcttgtgagtccgcacgggtaggtaccaccactccgtctatttctgccctgaagcagcattgcgtttcggtttgaaaggtggggtagccgtggtaactatactatactatagtaattccaaaattcgctgatttatgttctattagtctgatttagttaaaccatttctatagttactatagttattacctttcttgtactgcacagagacacggaatgctgttttattttaagttttgagttattatagtttaataaatactgtcatattacataattatttatgtgcaagatgtaatggccatttagatgtgatacgtcctttttacaaaaaaaaaacatgctatatgaaaaaaaaaaaaaaaaaaa6PastesequencePasteyoursequencehere.71）ChangefontsizeClickhere.82）ChangeLayout(1/2)Clickhere.9ChangeLayout(2/2)Thenclickhere.Clickhere.10Thechangedlayout113）ChangetoUPPERCASEClickhere.12ChangetouppercaseClickhere.13Thechangedletters144）FindORF将光标放到第1个碱基上Clickhere.15FindORFClickhere.16ThefoundORF175）TranslateDNAClickhere.18Resultof“translateDNA”196）Selectnucleotides204.1.2PrimerSelect开始→程序→DNAStar→PrimerSelectClickhere.21Example4-2以克隆载体pBR322为模板DNA序列，设计引物用来扩增位于2013-2169位的H-strandYeffector。221）创建PrimerSelect文件Clickhere.23EntersequenceClickhere.24Entersequence1)Clickhere.2)Clickhere.3)Clickhere.25Blockview26SequenceviewClickhere.272）定义引物特点和位置Clickhere.28Primercharacteristics使用默认值，点击“OK”。29Primerlocations(1/4)Clickhere.30Primerlocations(2/4)Clickhere.Select“Upperandlowerprimerranges”.31Primerlocations(3/4)Clickhere.输入相应数值32Primerlocations(4/4)333）寻找引物对Clickhere.34Listofprimers按住圆圈往左移35对引物的评价Clickhere.Clickhere.36Alternateproducts线条越粗，能扩增出的产物量越大（第1对引物）。37Alternateproducts线条不是很粗，扩增出的产物量较少（第2对引物）。38错配点394）查看引物的其他信息再点击这里先选定第一对引物40Amplificationsummary41Compositionsummary(1/2)Clickhere.42Compositionsummary(2/2)43Primerselfdimers(1/2)Clickhere.44Primerselfdimers(2/2)45Primerpairdimers(1/2)Clickhere.46Primerpairdimers(2/2)47Primerhairpins(1/2)Clickhere.48Primerhairpins(2/2)