IPI-International Protein Index 数据库介绍 - 中国生物VIP专享VIP免费

IPI-InternationalProteinIndex数据库介绍俞鸿yuhong@biosino.com.cnyuhong@scbit.orgIPI-InternationalProteinIndex•EMBL-EBI•URL：http://www.ebi.ac.uk/IPI/IPIhelp.html•IPIprovidesatoplevelguidetothemaindatabasesthatdescribetheproteomesofhighereukaryoticorganisms•常使用在质谱的搜库计算算法（Algorithm）•IPI是以蛋白质相似性为基础的不同数据库之间通过映射产生的•两个关键问题–数据库之间如何进行匹配–每个数据集映射结果如何合并到一个数据集中流程下载序列数据数据库所有序列两两之间相似性比对互为最佳匹配的蛋白对匹配百分比要求大于95%所有最佳匹配的蛋白对组成一个类类IPI孤立蛋白已有类的部分片段非有类的部分片段SwissprotRefseqEnsemblTrEMBL聚类互为最佳匹配蛋白对DatabaseBDatabaseAa1,a2,a3….b1,b2,b3….a1与databaseB中所有蛋白比对后，得到与a1比对的最佳的为b1b1与databaseA中所有蛋白比对后，得到与a1比对的最佳的为a1a1,b1为互为最佳蛋白的蛋白对IPI序列的确定•IPI的序列采用以下数据库的优先级来选取Swissprot/Refseq/TrEMBL/Ensembl,前题是类中如果有小片段序列，那么所选取的序列必须能包括小片段序列MSIPI•MSIPIisadatabasederivedfromIPIcontainingadditionalinformationaboutcSNPsandN-terminalpeptidesinaformatsuitableforeasyuseinmassspectrometrysearchengines.MSIPIisavailableinthedirectoryftp://ftp.ebi.ac.uk/pub/databases/IPI/msipi.物种资源•Human•Mouse•Rat•Zebrafish•Arabidopsis•Chicken•Cow数据检索FTP数据资源•当前版本：ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/•旧版本：ftp://ftp.ebi.ac.uk/pub/databases/IPI/old/数据文件•Ipi.HUMAN.dat.gz•Ipi.HUMAN.fasta.gz•Ipi.HUMAN.history.gz•Ipi.HUMAN.IPC.gz•Ipi.HUMAN.mysql.gz•Ipi.HUMAN.xrefs.gz•Gi2ipi.xrefs.gz•Ipi.gene.HUMAN.xrefs.gz数据格式-UniProt•*.dat.gzIDIPI00003881.5IPI;PRT;415AA.ACIPI00003881;DT01-OCT-2001(IPIHumanrel.2.00,Created)DT06-OCT-2005(IPIHumanrel.3.11,Lastsequenceupdate)DESIMILARTOHETEROGENEOUSNUCLEARRIBONUCLEOPROTEINH.OSHomosapiens(Human).OCEukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;OCMammalia;Eutheria;Primates;Catarrhini;Hominidae;Homo.OXNCBI_TaxID=9606;CC-!-CHROMOSOME:10.CC-!-STARTCO-ORDINATE:43201071.CC-!-ENDCO-ORDINATE:43224620.DRUniProtKB/Swiss-Prot;P52597;HNRPF_HUMAN;-.CommentsDRVega;OTTHUMP00000019482;OTTHUMG00000018029;M.DRVega;OTTHUMP00000043413;OTTHUMG00000018029;-.DRVega;OTTHUMP00000043414;OTTHUMG00000018029;-.DRREFSEQ_REVIEWED;NP_004957;GI:4826760;-.DRUniProtKB/TrEMBL;Q5T0N2;Q5T0N2_HUMAN;-.DRUniProtKB/TrEMBL;Q8NI96;Q8NI96_HUMAN;-.DRUniProtKB/TrEMBL;Q96AU2;Q96AU2_HUMAN;-.DRENSEMBL;ENSP00000338477;ENSG00000169813;-.DRENSEMBL;ENSP00000348345;ENSG00000169813;-.DRH-InvDB;HIT000003838;HIX0008779;-.DRH-InvDB;HIT000030409;HIX0008779;-.DRH-InvDB;HIT000031821;HIX0008779;-.DRH-InvDB;HIT000037199;HIX0008779;-.DRH-InvDB;HIT000037659;HIX0008779;-.DRUniParc;UPI0000000C5C;-;-.DRHGNC;5039;HNRPF;-.DREntrezGene;3185;HNRPF;-.DRUniGene;Hs.808;-;-.DRCCDS;CCDS7204.1;-;-.DRReAlSpliceprotein;SL0000062;hnRNPF;factorinvolvedinalternativesplicing.DRtrome;HTR002991;-;-.DRRZPD;Hs.808;-;Clonesandotherresearchmaterial.DRCleanEx;HS_HNRPF;-;-.DRInterPro;IPR012677;a_b_plait_nuc_bd.DRInterPro;IPR000504;RNP1_RNA_bd.DRInterPro;IPR012996;Znf_CHHC.DRPfam;PF00076;RRM_1;3.DRPfam;PF08080;zf-RNPHF;1.DRSMART;SM00360;RRM;3.DRPROSITE;PS50102;RRM;2.DRGENE3D;G3D.3.30.70.330;Nucl_bd_a/b_plat;3.SQSEQUENCE415AA;45672MW;D14E170631FB1F31CRC64;MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADSANDGFVRLRGLPFGCTK...