生物信息学作业1.doc

生物信息学实验作业试验一一找到编码拟南芥（arabidopsis）phyA（光敏色素A）基因的核酸序列编号, 并记录查找过程。GI：224576211步骤1 进入NCBI主页2 搜索 arabidopsis phyA3 Arabidopsis thaliana phytochrome A (PHYA) gene, partial cds4 VERSION：GI：224576211二以phyA为检索词，在pubmed数据库中分别检索在题目和关键词字段中含有该检索词的文献，记录检索出的条目数目。Results: 614三仔细阅读所查询核酸序列在NCBI和EMBL数据库中格式的解释，理解各字段的含义，并比较NCBI与EMBL中序列格式的异同。EMBLNCBI含义IDLOCUS 序列简单说明DEDEFINITION序列简单描述ACACCESSION序列编号SVVERSION序列版本号KWKEYWORDS关键词OSSOURCE序列来源的物种名OCORGANISM序列来源的物种学名和分类地位RNREFERENCE相关文献编号，或递交序列的注册信息RAAUTHORS相关文献作者，或递交序列的作者RTTITLE相关文献题目RLJOURNAL相关文献刊物杂志名,或递交序列的作者单位PUBMED相关文献PudMed数据库编号RX相关文献Medline引文代码RC相关文献注释RP相关文献其它注释CC关于序列的注释信息DR相关数据库交叉引用号FHFEATURES序列特征表起始FT序列特征表子项SQ碱基种类统计数空格ORIGIN序列实验二一 分析你感兴趣核酸序列的分子质量、碱基组成。Composition 35 A; 25 C; 35 G; 15 T; 0 OTHERPercentage: 32% A; 23% C; 32% G; 14% T; 0%OTHERMolecular Weight (kDa): ssDNA: 34.26 dsDNA: 67.8二 列出你所分析核酸序列（或部分序列）的互补序列、反向序列、反向互补序列、DNA双链序列和RNA序列。R S1 ACTACTCGAG AAGCAGCGAC AGAGGCGTTA GCCCGCTCAG CAGACTGGCA GTTCTCTACC61 GACAAAAAAG AGGTAGGAGG CACAGTAATG ATACAGGCGT AGCAGGAGGGC S1 CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC61 TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGCTT CTCGAGTAGTR C S1 TGATGAGCTC TTCGTCGCTG TCTCCGCAAT CGGGCGAGTC GTCTGACCGT CAAGAGATGG61 CTGTTTTTTC TCCATCCTCC GTGTCATTAC TATGTCCGCA TCGTCCTCCCD DNA S1 GGGAGGACGA TGCGGACATA GTAATGACAC GGAGGATGGA GAAAAAACAG CCATCTCTTG CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC61 ACGGTCAGAC GACTCGCCCG ATTGCGGAGA CAGCGACGAA GAGCTCATCA TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGCTT CTCGAGTAGTRNA S1 GGGAGGACGA UGCGGACAUA GUAAUGACAC GGAGGAUGGA GAAAAAACAG CCAUCUCUUG61 ACGGUCAGAC GACUCGCCCG AUUGCGGAGA CAGCGACGAA GAGCUCAUCA三.列出核酸序列的限制性酶切位点分析结果（酶及识别位点）。Restriction analysis on USMethylation: dam-No dcm-NoScreened with 117 enzymes, 5 sites foundEcl136II 1 GAG/CTC 103 EcoICRI 1 GAG/CTC 103 SacI 1 GAGCT/C 105 SapI 1 GCTCTTCN/ 93 SstI 1 GAGCT/C 105 List by Site Order93 SapI 103 Ecl136II 105 SstI 105 SacI103 EcoICRI Non Cut EnzymesAatII Acc65I AccIII AclI AflII AgeIAhaIII Alw44I AlwNI ApaBI ApaI ApaLIAscI Asp718I AsuII AvrII BalI BamHIBbeI BbvII BclI BglI BglII Bpu1102IBsc91I BsiI BsmI Bsp1407I BspHI BspMIBspMII BssHII BstD102I BstEII BstXI Bsu36IClaI Csp45I CspI CvnI DraI DraIIIDrdI EagI Eam1105I Eco31I Eco47III Eco52IEco56I Eco57I Eco72I EcoNI EcoRI EcoRVEheI EspI FseI HindIII HpaI I-PpoIKpnI MfeI Mlu113I MluI MscI MstIMstII NaeI NarI NcoI NdeI NheINotI NruI NsiI PacI PflMI PinAIPmaCI PmeI PstI PvuI PvuII RleAISacII SalI SauI ScaI SciI SfiISgrAI SmaI SnaBI SpeI SphI SplISpoI SrfI SspI SstII StuI SunISwaI Tth111I VspI XbaI XcmI XhoIXmaI XmaIII XmnI XorII Restriction sites on US1 GGGAGGACGATGCGGACATAGTAATGACACGGAGGATGGAGAAAAAACAGCCATCTCTTG SacI SstI Ecl136II SapI EcoICRI61 ACGGTCAGACGACTCGCCCGATTGCGGAGACAGCGACGAAGAGCTCATCA四分析一对你所设计的引物，并对其进行综合评判。2 GGAGGACGATGCGGACATAOligo: 5-GGAGGACGATGCGGACATA-3Primer1: 19 basesComposition 6 A; 3 C; 8 G; 2 T; 0 OTHERPercentage: 31% A; 15% C; 42% G; 10% T; 0%OTHERMW=5.99 kDaHybridization: D:DSalt: 50 mMFormamide: 0%Mismatch: 0 bpThermo Tm = 62.0 Hybridization Tm = 52.1 GC+AT Tm = 60.0Primer-US(1-110) complementarity.First complementarity in continuous: 19 bp5-GGAGGACGATGCGGACATA-3 Primer |3-CCTCCTGCTACGCCTGTAT-5 (20) Strand -No second possible complementarityMax complementarity in discontinuous: 19 bp5-GGAGGACGATGCGGACATA-3 Primer |3-CCTCCTGCTACGCCTGTAT-5 (20) Strand -105 AGCTCTTCGTCGCTGTCTCCOligo: 5-AGCTCTTCGTCGCTGTCTCC-3Primer1: 20 basesComposition 1 A; 8 C; 4 G; 7 T; 0 OTHERPercentage: 5% A; 40% C; 20% G; 35% T; 0%OTHERMW=6.07 kDaHybridization: D:DSalt: 50 mMFormamide: 0%Mismatch: 0 bpThermo Tm = 62.2 Hybridization Tm = 54.5 GC+AT Tm = 64.0Primer-US(1-110) complementarity.First complementarity in continuous: 20 bp5-AGCTCTTCGTCGCTGTCTCC-3 Primer |3-TCGAGAAGCAGCGACAGAGG-5 (86) Strand +No second possible complementarityMax complementarity in discontinuous: 20 bp5-AGCTCTTCGTCGCTGTCTCC-3 Primer |3-TCGAGAAGCAGCGACAGAGG-5 (86) Strand +五运用Sequin软件进行序列提交，并打印你完成的序列提交文件（后缀为.sqn）。LOCUS GY482612 110 bp mRNA linear UNA 17-FEB-2002DEFINITION Sequence 33 from patent US 8030290.ACCESSION GY482612VERSION GY482612.1 GI:353292184KEYWORDS .SOURCE unidentified ORGANISM unidentified unclassified sequences.REFERENCE 1 (bases 1 to 110) AUTHORS chen,h. TITLE Sequence 33 from patent US 8030290 JOURNAL UnpublishedREFERENCE 2 (bases 1 to 110) AUTHORS chen,h. TITLE Direct Submission JOURNAL Submitted (17-FEB-2002) SCAU, Bio, yucheng, yanan, sichuan, ChinaiFEATURES Location/Qualifiers