生物信息学实验报告 - 图文

生物信息学实验报告

姓名：__黄栋_______

学号：___030940119____

指导老师：___宋晓峰____

南京航空航天大学 2011年11月

1

实验一 生物信息数据库的检索

一．实验目的：

1.了解生物信息学的各大门户网站以及其中的主要资源。 2.了解主要数据库的内容及结构，理解各数据库注释的含义。 3.以PubMed为例，学会文献数据库的基本查询检索方法。

二．实验内容：

（1）国际与国内的生物信息中心

国际NCBI、EBI、ExPASy，EMBL、SIB、TIGR以及国内CBI、BioSino网站的熟悉及内容的了解。

核酸序列数据库：genbank/EMBL-bank/DDBJ NCBI网址：http://www.ncbi.nlm.nih.gov/ EBI网址：http://www.ebi.ac.uk/

EMBL网址：http://www.ebi.ac.uk/embl

蛋白质序列数据库：

Swiss Prot 、ExPASy网址：http://expasy.org/ Uniprot网址：http://www.uniprot.org/

蛋白质结构数据库：

PDB网址：http://www.rcsb.org/pdb/ （2）检索练习：

The spike protein of SARS-Corona Virus在NCBI中的核酸记录序列：

LOCUS CS244439 3897 bp DNA linear PAT 17-JUL-2006

DEFINITION Sequence 3 from Patent WO2005118813. ACCESSION CS244439

VERSION CS244439.1 GI:84659113 KEYWORDS .

SOURCE SARS coronavirus ORGANISM SARS coronavirus

Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirinae; Betacoronavirus. REFERENCE 1

AUTHORS Altmeyer,R., Nal-Rogier,B., Chan,C., Kien,F., Kam,Y.W., Siu,Y.L., Tse,K.S., Staropoli,I. and Manuguerra,J.C.

TITLE Nucleic acids, polypeptides, methods of expression, and immunogenic compositions associated with sars corona virus spike protein JOURNAL Patent: WO 2005118813-A2 3 15-DEC-2005;

INSTITUT PASTEUR (FR); Hong Kong Pasteur Research Centre Limited (CN)

FEATURES Location/Qualifiers source 1..3897

2

/organism=\ /mol_type=\ /db_xref=\ CDS 44..3847

/note=\ /codon_start=1

/protein_id=\ /db_xref=\

/translation=\TLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYTGPGGDYKDDDDK\

ORIGIN

1 ctatagggcg aattgggtac cgctagcgga tccgcgcgcc accatgttta ttttcctgct 61 gtttctgact ctgaccagcg gcagtgacct ggaccggtgc accacttttg atgatgtgca 121 ggctcctaat tacactcagc atacttcctc tatgaggggc gtgtactatc ctgatgaaat 181 ttttagatcc gacactctgt atctgactca ggatctgttt ctgccattct attctaatgt 241 gacaggcttt catactatta atcatacctt tggcaaccct gtgatccctt ttaaggatgg 301 catctatttt gctgccacag agaagtccaa tgtggtgcgg ggatgggtgt tcggctctac 361 catgaacaac aagtcccagt ccgtgattat tattaacaat tctactaatg tggtgatccg 421 agcctgtaac tttgaactgt gtgacaaccc attctttgct gtgtctaagc ccatgggcac 481 acagacacat actatgatct tcgataatgc ctttaattgc actttcgagt acatctctga 541 tgccttttcc ctggatgtgt ccgaaaagtc cggcaacttt aagcacctgc gagagtttgt 601 gtttaagaat aaggatggct ttctgtatgt gtataagggc tatcagccta tcgacgtggt 661 gcgcgatctg ccttctggct ttaacactct gaagcctatt tttaagctgc ctctgggcat

3

721 taacattaca aattttcggg ccattctgac agcctttagc cctgctcagg acatttgggg 781 cacctctgct gccgcctatt ttgtgggcta tctgaagcca actaccttta tgctgaagta 841 tgatgaaaat ggcacaatca cagatgctgt ggattgttct cagaatccac tggctgaact 901 gaagtgctct gtgaagagct ttgagattga caagggaatc taccagacct ctaatttccg 961 cgtggtgccc tctggagatg tggtgagatt ccctaatatt acaaacctgt gtccttttgg 1021 agaagtgttt aatgctacta agttcccttc tgtgtatgcc tgggagagaa agaagatttc 1081 taattgtgtg gctgattact ctgtgctgta caactccaca ttttttagca cctttaagtg 1141 ctatggcgtg tctgccacta agctgaatga tctgtgcttc tccaatgtgt atgccgattc 1201 ttttgtggtg aagggagatg atgtgagaca gatcgcccca ggacagactg gcgtgattgc 1261 tgattacaat tataagctgc cagatgattt catgggctgt gtgctggctt ggaatactag 1321 gaacattgat gctacttcca ctggcaatta taattacaag tatcggtatc tgagacatgg 1381 caagctgagg ccctttgaga gagacatctc taacgtgcct ttcagccctg atggcaagcc 1441 ttgcacccca cctgctctga attgttattg gccactgaat gattatggct tttacaccac 1501 tactggcatt ggctaccagc cttacagagt ggtggtgctg tcttttgaac tgctgaatgc 1561 ccctgccaca gtgtgtggac caaagctgtc cactgacctg attaagaacc agtgtgtgaa 1621 ctttaacttt aatggactga ctggcactgg cgtgctgact ccttctagca agagatttca 1681 gccatttcag cagtttggcc gggatgtgtc tgatttcact gattccgtgc gagatcctaa 1741 gacatctgaa atcctggaca tttccccttg ctcttttggc ggcgtgagcg tgattacacc 1801 tggaacaaat gcttcctctg aagtggctgt gctgtatcag gatgtgaact gcactgatgt 1861 gtctacagcc atccatgccg atcagctgac accagcttgg cgcatctatt ctactggaaa 1921 caatgtgttc cagactcagg ccggctgtct gatcggagct gagcatgtgg acacttctta 1981 tgagtgcgac attcctattg gagctggcat ttgtgctagt taccatacag tgtctctgct 2041 gcggagtact agccagaagt ctattgtggc ttatactatg tctctgggcg ctgatagttc 2101 cattgcttac tctaataaca ccattgctat ccctactaac ttttccatta gcattactac 2161 agaagtgatg cctgtgtcta tggctaagac ctccgtggat tgtaatatgt acatctgcgg 2221 agattctacc gaatgtgcta atctgctgct gcagtatggc agcttttgca cacagctgaa 2281 tcgggctctg tctggcattg ctgctgaaca ggatcgcaac acacgggaag tgttcgctca 2341 agtgaagcag atgtataaga ccccaactct gaagtatttt ggcggcttta atttttccca 2401 gatcctgcct gaccctctga agcccactaa gcggtctttt attgaggacc tgctgtttaa 2461 caaagtgaca ctggctgatg ctggctttat gaagcagtat ggcgaatgcc tgggcgatat 2521 taatgctaga gatctgattt gtgcccagaa gttcaatggc ctgacagtgc tgcctcctct 2581 gctgactgat gatatgattg ctgcctacac tgctgctctg gtgtctggca ctgccactgc 2641 tggatggaca tttggcgctg gcgctgctct gcagatccct tttgctatgc agatggccta 2701 tcggttcaat ggcattggag tgacccagaa tgtgctgtat gagaaccaga agcagattgc 2761 caaccagttt aacaaggcca ttagtcagat tcaggaatcc ctgacaacaa catccactgc 2821 cctgggcaag ctgcaggacg tggtgaacca gaatgctcag gccctgaaca cactggtgaa 2881 gcagctgagc agcaattttg gcgccatttc cagtgtgctg aatgatatcc tgtcccgact 2941 ggataaagtg gaggccgaag tgcagattga caggctgatt acaggcagac tgcagagcct 3001 gcagacctat gtgacacagc agctgatcag ggctgctgaa atcagggctt ctgccaatct 3061 ggctgctact aagatgtctg agtgtgtgct gggacagtcc aagagagtgg acttttgtgg 3121 aaagggctac cacctgatgt ccttcccaca ggctgcccct catggagtgg tgttcctgca 3181 tgtgacctat gtgccatccc aggagaggaa cttcaccaca gccccagcca tttgtcatga 3241 aggcaaggcc tacttccctc gggaaggcgt gttcgtgttt aatggcactt cttggtttat 3301 tacacagcgg aacttcttta gcccacagat catcactaca gacaatacat ttgtgtccgg

4