生物信息上机作业

生物信息学上机作业一 生物信息数据库信息检索上机内容：1、了解NCBI、DDBJ、EMBL上网的方法自学各网站相关介绍。NCBI(/):是指美国国立生物技术信息中心。理解自然无声但精妙的关于生命细胞的语言是现代分子生物学的要求。DDBJ（http:/www.ddbj.nig.ac.jp/）：日本DNA数据库，DDBJ(DNA Data Bank of Japan)，于1984年建立，是世界三大DNA 数据库之一，与NCBI的GenBank，EBI的EMBL数据库共同组成国际DNA数据库EMBL（http:/www.ebi.ac.uk/）：欧洲分子生物学实验室EMBL（The European Molecular Biology Laboratory），于1974年由欧洲14个国家加上亚洲的以色列共同发起建立，包括一个位于德国Heidelberg的核心实验室，及三个位于德国Hamburg，法国Grenoble及英国Hinxton的研究分部。2、 了解北大生物信息学中心等几大中文生物信息学网站。北京大学 生物信息中心/复旦大学 理论生物中心：http:/tlife.fudan,/天津大学 生物信息中心：/上海生物信息技术研究中心：/index.php3、 了解一些生物论坛中有关生物信息学的部分。如：生物秀、生物谷生物信息学生物秀/生物谷/bioinfo.htm 4、利用NCBI的Entrenz查询系统索文献和核酸或蛋白质序列。（phyA）并对照所学复习各字段的含义。PU4_plate12_D18 PU4 Prunus persica cDNA similar to identical to photoreceptor PHYA (PHYA) gene Prunus persica, mRNA sequenceGenBank: DY649091.1GenBank FASTA IDENTIFIERSdbEST Id: 37221463EST name: PU4_plate12_D18GenBank Acc: DY649091GenBank gi: 89493297CLONE INFOSource: Herman Silva (hsilvaunab.cl)Insert length: 631DNA type: cDNAPRIMERSPCR forward: GTAAAACGACGGCCAGTAGAPCR backward: TAGGAAACAGCTATGACCATSequencing: M13FWD = GTAAAACGACGGCCAGTPolyA Tail: UnknownSEQUENCECTCAGGCTTCGCGGTTCCTATTTATGAAGAATAAGGTCCGAATGATTGTTGACTGTTGTGCAAAACAGGTGAAGGTGCTTCAAGATGAGAAGCTTCCATTTGATCTCACATTGTGCGGTTCAACCCTAAGATCCCCACATAGTTGCCATTTACAATATATGAAGAATATGGAATCTATTGCATCTCTTGTTATGGCAGTAGTGGTTAACGAGGGGGATGATGAGGTAGCCAGTCCTGATTCTGTTCAGCCTCAAAAAAGAAAGAGACTTTGGGGTTTGGTAGTATGTCATAATACAAGTCCAAGATTTGTTCCTTTCCCTCTCAGGTATGCCTGTGAGTTTCTAGCTCAAGTATTTGCCATCCATGTCAATAAGGAAATAGAGTTGGAAGATCAGATGGTTGAGAAGAACATCCTGCGCACCCAAACGCTGTTGTGTGATATGTTGTTACGAGATGCACCCTTGGGTATTGTGTCACAGAGCCCTAATATTATGGATCTAGTGAAATGTGATGGAGCTGCCCTATTATACAAGAGCAAGATATGGAGACTTGGCATAACTCCAAGTGACTTCCAGCTTCATGACATAGCCTCGTGGCTCG CTGAGTACCATATGGATTCCACAGGTTTGAGEntry Created: Mar 13 2006Last Updated: Mar 13 2006COMMENTS Consortium: Chilean Functional Genomics in Prunus persica. The members of this Consortium are University of Chile, Instituto de Investigaciones Agropecuarias (INIA), Asociacion de Exportadores (ASOEX), Fundacion para el Desarrollo Fruticola (FDF) and Fundac on Chile. This Consortium was formed as part of the Chilean Genome Initiative and supported by FDI-CORFO (FDI G02 P1001)PUTATIVE ID Assigned by submitter identical to photoreceptor PHYA (PHYA) gene Prunus persicaLIBRARYLib Name: LIBEST_019257 PU4Organism: Prunus persicaCultivar: OHenryOrgan: FruitTissue type: MesocarpLab host: DH10B E.coliVector: pDNR-1rR. Site 1: XhoIR. Site 2: SmaISUBMITTERName: Herman SilvaLab: Center of Plant BiotechnologyInstitution: Andres Bello UniversityAddress: Av. Republica 217, 837-0146 Santiago, ChileTel: 56-2-6618648Fax: 56-2-6615832E-mail: hsilvaunab.clCITATIONSTitle: ESTs sequences isolated from peachesAuthors: Silva,H., Loira,N., Vizoso,P., Latorre,M., Baeza-Yates,R., Cambiazo,V., Campos-Vargas,R., Gonzalez,M., Orellana,A., Retamales,J., Meisel,L.Year: 2005Status: Unpublished5、中科院计算所智能信息处理重点上机室生物信息学:/index.php6、找到编码人（zwintI）基因的核酸序列编号。NM_001005413二 核酸及蛋白质序列的比对一、上机内容利用检索出的蛋白质和核酸序列进行序列比对并进行分子进化树分析。二、作业1、绘制分子进化树，并标明各个物种phyA蛋白之间的序列相似性。2、根据你所学生物分类的知识，试解释该分子进化树的合理性拟南芥：植物界 种子植物门 被子植物门 双子叶植物纲 十字花目 十字花科 鼠耳芥属（拟南芥属）大豆：植物界 种子植物门 被子植物亚门 双子叶植物纲 豆目 蝶形花科 大豆属 血红肉果兰：植物界 种子植物门 被子植物亚门 百合纲 百合目 兰科 树兰亚科 肉果兰属水稻：植物界 种子植物门 被子植物亚门 单子叶植物纲 禾本目 禾本科 稻属 玉米：植物界 种子植物门 被子植物亚门 单子叶植物纲 禾本目 禾本科 玉米属高粱：植物界 种子植物门 被子植物亚门 单子叶植物纲 禾本目 禾本科 高粱属经过对比可得下列同源性关系高粱玉米水稻拟南芥大 豆血红肉果兰与前面的同源树对比基本相似，说明软件分析结果与实际相符3、找出一条可能的保守序列（多条蛋白共同的氨基酸序列）。最长的保守序列： kliqpfgcllaldek三 核酸序列分析一、上机内容1、 使用DNAstar进行核酸基本信息分析2、ORF分析二、作业1、记录人（zwintI）基因 序列的序列组成2、 记录人（zwintI）基因 序列最长的ORF的起止区间。使用Editseq软件进行查找ORF序列LOCUS NM_001005413 1546 bp mRNA linear PRI 12-FEB-2014DEFINITION Homo sapiens ZW10 interacting kinetochore protein (ZWINT), transcript variant 3, mRNA.ACCESSION NM_001005413VERSION NM_001005413.1 GI:53729319KEYWORDS RefSeq.SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.REFERENCE 1 (bases 1 to 1546) AUTHORS Endo H, Ikeda K, Urano T, Horie-Inoue K and Inoue S. TITLE Terf/TRIM17 stimulates degradation of kinetochore protein ZWINT and regulates cell proliferation JOURNAL J. Biochem. 151 (2), 139-144 (2012) PUBMED 22023800 REMARK GeneRIF: the E3 ubiquitin ligase terf causes protein degradation of ZWINT and negatively regulates cell proliferationREFERENCE 2 (bases 1 to 1546) AUTHORS Kasuboski JM, Bader JR, Vaughan PS, Tauhata SB, Winding M, Morrissey MA, Joyce MV, Boggess W, Vos L, Chan GK, Hinchcliffe EH and Vaughan KT. TITLE Zwint-1 is a novel Aurora B substrate required for the assembly of a dynein-binding platform on kinetochores JOURNAL Mol. Biol. Cell 22 (18), 3318-3330 (2011) PUBMED 21775627 REMARK GeneRIF: These studies identify zwint-1 as a novel AurB substrate required for kinetochore assembly and for proper spindle assembly checkpoint silencing at metaphaseREFERENCE 3 (bases 1 to 1546) AUTHORS Vos LJ, Famulski JK and Chan GK. TITLE hZwint-1 bridges the inner and outer kinetochore: identification of the kinetochore localization domain and the hZw10-interaction domain JOURNAL Biochem. J. 436 (1), 157-168 (2011) PUBMED 21345172 REMARK GeneRIF: hZwint-1 bridges the inner and outer kinetochore: identification of the kinetochore localization domain and the hZw10-interaction domainREFERENCE 4 (bases 1 to 1546) AUTHORS Parsa A, Chang YP, Kelly RJ, Corretti MC, Ryan KA, Robinson SW, Gottlieb SS, Kardia SL, Shuldiner AR and Liggett SB. TITLE Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality JOURNAL Clin Transl Sci 4 (1), 17-23 (2011) PUBMED 21348951REFERENCE 5 (bases 1 to 1546) AUTHORS Brendle A, Brandt A, Johansson R, Enquist K, Hallmans G, Hemminki K, Lenner P and Forsti A. TITLE Single nucleotide polymorphisms in chromosomal instability genes and risk and clinical outcome of breast cancer: a Swedish prospective case-control study JOURNAL Eur. J. Cancer 45 (3), 435-442 (2009) PUBMED 19008095 REMARK GeneRIF: Observational study of gene-disease association. (HuGE Navigator)REFERENCE 6 (bases 1 to 1546) AUTHORS Wang H, Hu X, Ding X, Dou Z, Yang Z, Shaw AW, Teng M, Cleveland DW, Goldberg ML, Niu L and Yao X. TITLE Human Zwint-1 specifies localization of Zeste White 10 to kinetochores and is essential for mitotic checkpoint signaling JOURNAL J. Biol. Chem. 279 (52), 54590-54598 (2004) PUBMED 15485811 REMARK GeneRIF: show that ZW10 interacting protein-1(Zwint-1) is required and is sufficient for kinetochore localization of Zeste White 10 (ZW10) in HeLa cellsREFERENCE 7 (bases 1 to 1546) AUTHORS Obuse C, Iwasaki O, Kiyomitsu T, Goshima G, Toyoda Y and Yanagida M.TITLE A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1 JOURNAL Nat. Cell Biol. 6 (11), 1135-1141 (2004) PUBMED 15502821REFERENCE 8 (bases 1 to 1546) AUTHORS Musio A, Mariani T, Montagna C, Zambroni D, Ascoli C, Ried T and Vezzoni P. TITLE Recapitulation of the Roberts syndrome cellular phenotype by inhibition of INCENP, ZWINT-1 and ZW10 genes JOURNAL Gene 331, 33-40 (2004) PUBMED 15094189REFERENCE 9 (bases 1 to 1546) AUTHORS Van Hooser AA, Ouspenski II, Gregson HC, Starr DA, Yen TJ, Goldberg ML, Yokomori K, Earnshaw WC, Sullivan KF and Brinkley BR. TITLE Specification of kinetochore-forming chromatin by the histone H3 variant CENP-A JOURNAL J. Cell. Sci. 114 (PT 19), 3529-3542 (2001) PUBMED 11682612REFERENCE 10 (bases 1 to 1546) AUTHORS Starr DA, Saffery R, Li Z, Simpson AE, Choo KH, Yen TJ and Goldberg ML.TITLE HZwint-1, a novel human kinetochore component that interacts withHZW10 JOURNAL J. Cell. Sci. 113 (PT 11), 1939-1950 (2000) PUBMED 10806105COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from BG615304.1, BM724168.1,BC020979.1 and BC016357.2. Summary: This gene encodes a protein that is clearly involved in kinetochore function although an exact role is not known. It interacts with ZW10, another kinetochore protein, possibly regulating the association between ZW10 and kinetochores. The encoded protein localizes to prophase kinetochores before ZW10 does and it remains detectable on the kinetochore until late anaphase. It has a uniform distribution in the cytoplasm of interphase cells. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. provided by RefSeq, Jul 2008. Transcript Variant: This variant (3) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. #Evidence-Data-START# Transcript exon combination : BX448627.2, AL557130.3 ECO:0000332 RNAseq introns : single sample supports all introns ERS025087, ERS025093 ECO:0000348 #Evidence-Data-END# COMPLETENESS: complete on the 3 end.PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-5 BG615304.1 1-5 6-46 BM724168.1 9-49 47-556 BC020979.1 34-543 557-1358 BC020979.1 685-1486 1359-1511 BC020979.1 1487-1639 1512-1519 BC016357.2 957-964 1520-1546 BC016357.2 1147-1173FEATURES Location/Qualifiers source 1.1546 /organism=Homo sapiens /mol_type=mRNA /db_xref=taxon:9606 /chromosome=10 /map=10q21-q22 gene 1.1546 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /note=ZW10 interacting kinetochore protein /db_xref=GeneID:11130 /db_xref=HGNC:HGNC:13195 /db_xref=HPRD:18366 /db_xref=MIM:609177 exon 1.78 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 CDS 38.730 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /note=isoform b is encoded by transcript variant 3; human ZW10 interacting protein-1; zwint-1; ZW10 interactor, kinetochore protein /codon_start=1 /product=ZW10 interactor isoform b /protein_id=NP_001005413.1 /db_xref=GI:53729320 /db_xref=CCDS:CCDS31205.1 /db_xref=GeneID:11130 /db_xref=HGNC:HGNC:13195 /db_xref=HPRD:18366 /db_xref=MIM:609177/translation=MEAAETEAEAAALEVLAEVAGILEPVGLQEEAELPAKILVEFVV DSQKKDKLLCSQLQVADFLQNILAQEDTAKGLDPLASEDTSRQKAIAAKEQWKELKATYREHVEAIKIGLTKALTQMEEAQRKRTQLREAFEQLQAKKQMAMEKRRAVQNQWQLQQEKHLQHLAEVSAEGKLLFPEAEAEAENLPDDKPQQPTRPQEQSTGDTMGRDPGVSFKAGLQPAGDVNLP exon 79.169 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 170.293 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 294.460 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 461.517 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 518.556 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 557.688 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 689.771 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 exon 772.1519 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /inference=alignment:Splign:1.39.8 STS 1361.1486 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 /standard_name=STS-H99221 /db_xref=UniSTS:22396 polyA_signal 1495.1500 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1 polyA_site 1519 /gene=ZWINT /gene_synonym=HZwint-1; KNTC2AP; ZWINT1ORIGIN 1 gattgtggga aggcagctga actcggcgcc tggaaagatg gaggcagcgg agacagaggc 61 ggaagctgca gccctagagg tcctggctga ggtggcaggc atcttggaac ctgtaggcct 121 gcaggaggag gcagaactgc cagccaagat cctggttgag tttgtggtgg actctcagaa 181 gaaagacaag ctgctctgca gccagcttca ggtagcggat ttcctgcaga acatcctggc 241 tcaggaggac actgctaagg gtctcgaccc cttggcttct gaagacacga gccgacagaa 301 ggcaattgca gctaaggaac aatggaaaga gctgaaggcc acctacaggg agcacgtaga 361 ggccatcaaa attggcctca ccaaggccct gactcagatg gaggaagccc agaggaaacg 421 gacacaactc cgggaagcct ttgagcagct ccaggccaag aaacaaatgg ccatggagaa 481 acgcagagca gtccagaacc agtggcagct acaacaggag aagcatctgc agcatctggc 541 ggaggtttct gcagagggta agctgttgtt ccctgaggct gaggctgagg cagagaatct 601 tccagatgat aaaccccagc agccgactcg accccaggag cagagtacag gagacaccat 661 ggggagagac cctggtgtgt ccttcaaggc tgttggtcta caacctgctg gagatgtaaa 721 tttgccatga cttcctggag gacagcagca tggagaaaga tcctagaaaa ggcctctgac 781 ttccctcacc tcccaaccat cattacagga aagactgtga actcctgagt tcagcttgat 841 ttctgactac atcccagcaa gctctggcat ctgtggatta aaatccctgg atctctctca 901 gttgtgtatt tgttcatctt catatgctgg caggaacaac tattaataca gatactcaga 961 agccaataac atgacaggag ctgggactgg tttgaacaca gggtgtgcag atggggaggg 1021 ggtactggcc ttgggcctcc tatgatgcag acatggtgaa tttaattcaa ggaggaggag 1081 aatgttttag gcaggtggtt at