生物信息概论上机作业答案.docx
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生物信息概论上机作业答案.docx
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生物信息概论上机作业答案
实验一
1.plk1和HOTAIR在乙肝病毒诱导肝脏癌变的过程中加速了对蛋白酶体SUZ12和ZNF198的降解。
在有乙肝病毒的细胞中,他会增加PLK1酶的表达,减少两个转录抑制子相互结合的比例。
作者研究发现:
plk1可诱导SUZ12和ZNF198的降解通过使特定位点的磷酸化,然后这个过程可以被HOTAIR增强,因为这种长的编码RNA可减少他们的稳定性。
---PLK1andHOTAIRaccelerateproteasomaldegradationofSUZ12andZNF198duringhepatitisBvirus-inducedlivercarcinogenesis.
2.胰岛素受体蛋白在生长因子刺激的跨膜信号转导过程中起重要作用。
在研究中,我们认为plk1可以使IRS2的两个丝氨酸(ser556和ser1098)磷酸化。
这两个氨基酸被磷酸化后可以抑制IRS2和PL3K途径复合物的结合并增加IRS2蛋白的降解速率,从而抑制PL3K途径的激活。
---Plk1 PhosphorylationofIRS2PreventsPrematureMitoticExitviaAKTInactivation.
3.Plk1在细胞的有丝分裂中扮演重要角色,在各种肿瘤细胞中都有很高的plk1水平,包括急性骨髓性白血病(AML),抑制plk1后,细胞会衰老和凋亡,并具有抗肿瘤效果。
所以,我们也开发了一种抑制plk1的药物volasertib 。
——Targetingpolo-likekinase1inacutemyeloidleukemia
4. Plk1和Aurora酶会调节细胞的有丝分裂,我们发现通过增强plk1抑制剂的浓度,也会增强对Aurora酶的抑制剂效果,从而抑制细胞的分裂,可作为癌细胞的治疗手段。
——Co-inhibitionofpolo-likekinase1andaurorakinasespromotesmitoticcatastrophe.
5.plk1在有丝分裂中管理DNA的断裂和修复
——Plk1 ManagesDNAbreakrepairduringmitosis.
二.核酸序列
Homosapienspolo-likekinase1(PLK1),mRNA
>gi|748982951|ref|NM_005030.4|Homosapienspolo-likekinase1(PLK1),mRNA
AGTGGCGCGCAGGCTTTTGTAACGTTCCCAGCGCCGCGTTTGAATTCGGGGAGGAGCGGAGCGGTGCGGA
GGCTCTGCTCGGATCGAGGTCTGCAGCGCAGCTTCGGGAGCATGAGTGCTGCAGTGACTGCAGGGAAGCT
GGCACGGGCACCGGCCGACCCTGGGAAAGCCGGGGTCCCCGGAGTTGCAGCTCCCGGAGCTCCGGCGGCG
GCTCCACCGGCGAAAGAGATCCCGGAGGTCCTAGTGGACCCACGCAGCCGGCGGCGCTATGTGCGGGGCC
GCTTTTTGGGCAAGGGCGGCTTTGCCAAGTGCTTCGAGATCTCGGACGCGGACACCAAGGAGGTGTTCGC
GGGCAAGATTGTGCCTAAGTCTCTGCTGCTCAAGCCGCACCAGAGGGAGAAGATGTCCATGGAAATATCC
ATTCACCGCAGCCTCGCCCACCAGCACGTCGTAGGATTCCACGGCTTTTTCGAGGACAACGACTTCGTGT
TCGTGGTGTTGGAGCTCTGCCGCCGGAGGTCTCTCCTGGAGCTGCACAAGAGGAGGAAAGCCCTGACTGA
GCCTGAGGCCCGATACTACCTACGGCAAATTGTGCTTGGCTGCCAGTACCTGCACCGAAACCGAGTTATT
CATCGAGACCTCAAGCTGGGCAACCTTTTCCTGAATGAAGATCTGGAGGTGAAAATAGGGGATTTTGGAC
TGGCAACCAAAGTCGAATATGACGGGGAGAGGAAGAAGACCCTGTGTGGGACTCCTAATTACATAGCTCC
CGAGGTGCTGAGCAAGAAAGGGCACAGTTTCGAGGTGGATGTGTGGTCCATTGGGTGTATCATGTATACC
TTGTTAGTGGGCAAACCACCTTTTGAGACTTCTTGCCTAAAAGAGACCTACCTCCGGATCAAGAAGAATG
AATACAGTATTCCCAAGCACATCAACCCCGTGGCCGCCTCCCTCATCCAGAAGATGCTTCAGACAGATCC
CACTGCCCGCCCAACCATTAACGAGCTGCTTAATGACGAGTTCTTTACTTCTGGCTATATCCCTGCCCGT
CTCCCCATCACCTGCCTGACCATTCCACCAAGGTTTTCGATTGCTCCCAGCAGCCTGGACCCCAGCAACC
GGAAGCCCCTCACAGTCCTCAATAAAGGCTTGGAGAACCCCCTGCCTGAGCGTCCCCGGGAAAAAGAAGA
ACCAGTGGTTCGAGAGACAGGTGAGGTGGTCGACTGCCACCTCAGTGACATGCTGCAGCAGCTGCACAGT
GTCAATGCCTCCAAGCCCTCGGAGCGTGGGCTGGTCAGGCAAGAGGAGGCTGAGGATCCTGCCTGCATCC
CCATCTTCTGGGTCAGCAAGTGGGTGGACTATTCGGACAAGTACGGCCTTGGGTATCAGCTCTGTGATAA
CAGCGTGGGGGTGCTCTTCAATGACTCAACACGCCTCATCCTCTACAATGATGGTGACAGCCTGCAGTAC
ATAGAGCGTGACGGCACTGAGTCCTACCTCACCGTGAGTTCCCATCCCAACTCCTTGATGAAGAAGATCA
CCCTCCTTAAATATTTCCGCAATTACATGAGCGAGCACTTGCTGAAGGCAGGTGCCAACATCACGCCGCG
CGAAGGTGATGAGCTCGCCCGGCTGCCCTACCTACGGACCTGGTTCCGCACCCGCAGCGCCATCATCCTG
CACCTCAGCAACGGCAGCGTGCAGATCAACTTCTTCCAGGATCACACCAAGCTCATCTTGTGCCCACTGA
TGGCAGCCGTGACCTACATCGACGAGAAGCGGGACTTCCGCACATACCGCCTGAGTCTCCTGGAGGAGTA
CGGCTGCTGCAAGGAGCTGGCCAGCCGGCTCCGCTACGCCCGCACTATGGTGGACAAGCTGCTGAGCTCA
CGCTCGGCCAGCAACCGTCTCAAGGCCTCCTAATAGCTGCCCTCCCCTCCGGACTGGTGCCCTCCTCACT
CCCACCTGCATCTGGGGCCCATACTGGTTGGCTCCCGCGGTGCCATGTCTGCAGTGTGCCCCCCAGCCCC
GGTGGCTGGGCAGAGCTGCATCATCCTTGCAGGTGGGGGTTGCTGTATAAGTTATTTTTGTACATGTTCG
GGTGTGGGTTCTACAGCCTTGTCCCCCTCCCCCTCAACCCCACCATATGAATTGTACAGAATATTTCTAT
TGAATTCGGAACTGTCCTTTCCTTGGCTTTATGCACATTAAACAGATGTGAATATTCAAAAAAAAAAAAA
AAA
三.蛋白质序列
>sp|P53350|PLK1_HUMANSerine/threonine-proteinkinasePLK1OS=HomosapiensGN=PLK1PE=1SV=1
MSAAVTAGKLARAPADPGKAGVPGVAAPGAPAAAPPAKEIPEVLVDPRSRRRYVRGRFLG
KGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFF
EDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLG
NLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSKKGHSFEVDVWSIGCI
MYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELL
NDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPLTVLNKGLENPLPERPREKEE
PVVRETGEVVDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDK
YGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLK
YFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTK
LILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRL
KAS
四.基因功能分析
定位:
16号染色体23678822---23690367
功能结构域:
Go注释信息:
ATP结合酶的激活
BLAST定位
五.三级结构信息(P53350)
http:
//www.uniprot.org/uniprot/P53350#structure
实验二
1.功能结构域分析
Pfam
SMART:
http:
//smart.embl-heidelberg.de/smart/show_motifs.pl?
ID=PLK1_HUMAN
Interpro:
http:
//www.ebi.ac.uk/interpro/protein/P53350
2.细胞亚定位分析
TargetP:
http:
//www.cbs.dtu.dk/cgi-bin/webface2.fcgi?
jobid=554216B8000076F516230FC3&wait=20
PSORT:
3.基因表达,变异和疾病相关等分析
Genecards表达:
变异:
疾病相关
http:
//www.genecards.org/cgi-bin/carddisp.pl?
gene=PLK1&search=d4d9ebcf3bdc0357e84713a3892aa432
GENATLAS
表达:
疾病
http:
//genatlas.medecine.univ-paris5.fr/fiche.php?
onglet=4&n=6525
4.翻译后修饰位点分析
Phospho.Elm
http:
//phospho.elm.eu.org/cgimodel.py
GPS:
http:
//gps.biocuckoo.org/wsresult.php
http:
//www.uniprot.org/uniprot/P53350(总)
实验三
BioGRID
HPRD
STRING
Perl程序
#!
/usr/bin/perl-w
openIN,"start.txt";
openOUT,">medite.txt";
openFINAL,">end.txt";
while(
chomp($_);
@b=split/\t/,$_;
foreach$_(@b){
printOUT"$_\n";}
}
print"outok\n";
#先把所有数据打断,成一竖条保存。
closeOUT;
openOUT,"medite.txt";
@m=
print"sortok";
#把一竖条数据排序。
my$i=0;
my@f;
my$zz=$#e;
$ps=pop(@e);unshift(@f,$ps);
print@f;
while($i<=$zz){
$s=pop(@e);
if($seq$f[0]){}
else{unshift(@f,$s);}
$i++;
print"$i\t";}
printFINAL@f;
#现将排好序的数组@e一个个打出来,放到新数组@f中,打出的元素为$s如果@f中没有,就插进去
#有就不动,最后将@f输出。
closeIN;
closeOUT;
closeFINAL
;
练习四
1.同源序列与蛋白质家族分析
Homosapiens:
1.RecName:
Full=Serine/threonine-proteinkinasePLK1;AltName:
Full=Polo-likekinase1;Short=PLK-1;AltName:
Full=Serine/threonine-proteinkinase13;Short=STPK13[Homosapiens]
SequenceID:
sp|P53350.1|PLK1_HUMAN
2.RecName:
Full=Serine/threonine-proteinkinasePLK3;AltName:
Full=Cytokine-inducibleserine/threonine-proteinkinase;AltName:
Full=FGF-induciblekinase;AltName:
Full=Polo-likekinase3;Short=PLK-3;AltName:
Full=Proliferation-relatedkinase[Homosapiens]
SequenceID:
sp|Q9H4B4.2|PLK3_HUMAN
3.RecName:
Full=Serine/threonine-proteinkinasePLK2;AltName:
Full=Polo-likekinase2;Short=PLK-2;Short=hPlk2;AltName:
Full=Serine/threonine-proteinkinaseSNK;Short=hSNK;AltName:
Full=Serum-induciblekinase[Homosapiens]
SequenceID:
sp|Q9NYY3.3|PLK2_HUMAN
4.RecName:
Full=Serine/threonine-proteinkinasePLK4;AltName:
Full=Polo-likekinase4;Short=PLK-4;AltName:
Full=Serine/threonine-proteinkinase18;AltName:
Full=Serine/threonine-proteinkinaseSak[Homosapiens]
SequenceID:
sp|O00444.3|PLK4_HUMAN
Musmusculus:
1.RecName:
Full=Serine/threonine-proteinkinasePLK1;AltName:
Full=Polo-likekinase1;Short=PLK-1;AltName:
Full=Serine/threonine-proteinkinase13;Short=STPK13[Musmusculus]
SequenceID:
sp|Q07832.2|PLK1_MOUSE
2.RecName:
Full=Serine/threonine-proteinkinasePLK3;AltName:
Full=Cytokine-inducibleserine/threonine-proteinkinase;AltName:
Full=FGF-induciblekinase;AltName:
Full=Polo-likekinase3;Short=PLK-3[Musmusculus]
SequenceID:
sp|Q60806.2|PLK3_MOUSE
3.RecName:
Full=Inactiveserine/threonine-proteinkinasePLK5;AltName:
Full=Polo-likekinase5;Short=PLK-5[Musmusculus]
SequenceID:
sp|Q4FZD7.1|PLK5_MOUSE
4.RecName:
Full=Serine/threonine-proteinkinasePLK2;AltName:
Full=Polo-likekinase2;Short=PLK-2;AltName:
Full=Serine/threonine-proteinkinaseSNK;AltName:
Full=Serum-induciblekinase[Musmusculus]
SequenceID:
sp|P53351.1|PLK2_MOUSE
5.RecName:
Full=Serine/threonine-proteinkinasePLK4;AltName:
Full=Polo-likekinase4;Short=PLK-4;AltName:
Full=Serine/threonine-proteinkinase18;AltName:
Full=Serine/threonine-proteinkinaseSak[Musmusculus]
SequenceID:
sp|Q64702.2|PLK4_MOUSE
Drosophilamelanogaster:
1.RecName:
Full=Serine/threonine-proteinkinasepolo[Drosophilamelanogaster]
SequenceID:
sp|P52304.2|POLO_DROME
Caenorhabditiselegans:
1.RecName:
Full=Serine/threonine-proteinkinaseplk-1;AltName:
Full=Polo-likekinase1[Caenorhabditiselegans]
SequenceID:
sp|P34331.3|PLK1_CAEEL
2.RecName:
Full=Serine/threonine-proteinkinaseplk-2;AltName:
Full=Polo-likekinase2[Caenorhabditiselegans]
SequenceID:
sp|Q9N2L7.1|PLK2_CAEEL
3.RecName:
Full=Serine/threonine-proteinkinaseplk-3;AltName:
Full=Polo-likekinase3[Caenorhabditiselegans]
SequenceID:
sp|Q20845.1|PLK3_CAEEL
Schizosaccharomycespombe:
1.RecName:
Full=Serine/threonine-proteinkinaseplo1[Schizosaccharomycespombe972h-]
SequenceID:
sp|P50528.1|PLO1_SCHPO
Saccharomycescerevisiae:
1.RecName:
Full=Cellcycleserine/threonine-proteinkinaseCDC5/MSD2[SaccharomycescerevisiaeS288c]
SequenceID:
sp|P32562.1|CDC5_YEAST
二.多序列比对
ClustalOmega
http:
//www.ebi.ac.uk/Tools/services/web/toolresult.ebi?
jobId=clustalw2-I20150514-143948-0334-50663174-es&analysis=alignments
MUSCLE:
三.进化树MEGA:
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