> >TPIS_ECOLI [P04790] "Triosephosphate isomerase (EC ) (TIM) MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM LGAQNVDLNLSGAFTGETSA
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- かずし さどひら
- 7 years ago
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1 BLAST cd cp r /mandara/lecture/takawaba/blast. cd BLAST WEB /mandara/lecture/takawaba/bin BLAST./SETUP.cshrc.cshrc.orig_before_bioinfo06.cshrc bash TA 1
2 > >TPIS_ECOLI [P04790] "Triosephosphate isomerase (EC ) (TIM) MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD AFAVIVKAAEAAKQA >gi ref NC_ Escherichia coli K12, complete genome AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC [ ] AGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTTTAGAGCAACGAGACACG GCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAAAAAACGCCTTAGTAAGTAT TTTTC 2
3 >Y431_METJA [Q57873] Hypothetical UPF0333 protein MJ0431. MGKMKILKKLLSKKGQLSMEVGVLVAAAVLVAIIAAYFYVKNAKSAVASAGNKSAAFINV TANKSQEYISNLSNI >Y420_TREPA [O83435] Hypothetical protein TP0420. MRRRIYEERGAVRQAGLAHVFEYQGGAAHTGAVQDSDWAVVMRGDIAITLVYAQPVSMPP VLPLPDFAFQACCSY >VF07_VARV [P33867] Protein F7. MTLVMGSCCGRFCDAKNKFKKDDIEEEGEGYCDYKNLNDLDEATRIEFGPLYIINEEKSD INTLDIKRRYRHAIESVYF >VCOX_BPHP1 [P51705] Regulatory protein cox. MSKQNAICINIHMEQPYMTREEFAKKLDVSTRTIDRLRQQGVLKCIKMKNDEGEETERGL VLVDLVAIAVRNAKNAFQI 3
![MRRRIYEERGAVRQAGLAHVFEYQGGAAHTGAVQDSDWAVVMRGDIAITLVYAQPVSMPP VLPLPDFAFQACCSY >VF07_VARV [P33867] Protein F7.](/docs-images/47/20505917/images/page_3.jpg "MTLVMGSCCGRFCDAKNKFKKDDIEEEGEGYCDYKNLNDLDEATRIEFGPLYIINEEKSD INTLDIKRRYRHAIESVYF >VCOX_BPHP1 [P51705] Regulatory protein cox.")
4 ./DotMatrix./DotMatrixHBA_HUMAN HBA_MOUSE 4
5 ./DotMatrixHBA_HUMAN HBB_HUMAN 5
6 X01 X02,,X08.ncbirc BLAST.ncbirc BLAST /home/is/takawaba/blastdb swissprot ecoli_aa Escherichia coli bsubt_aa Bacillus subtilis mgeni_aa Mycoplasma genitalium 6
7 blastall blastp blastall p blastp d i o blastall p blastp d ecoli_aa i X01 o X01.ecoli less X01.ecoli blastall p blastp d ecoli_aa i X01 o X01.ecoli blastall p blastp d bsubt_aa i X01 o X01.bsubt blastall p blastp d mgeni_aa i X01 o X01.mgeni blastall p blastp d swissprot i X01 o X01.sws X02,X03,...X08 7
8 8
9 9
10 10
11 ftp.ncbi.nlm.nih.gov ftp://ftp.ncbi.nlm.nih.gov blast ia32-linux.tar.gz blast ia32-solaris.tar.gz blast ia32-win32.exe blast ppc32-maxosx.tar.gz gunzip blast ia32-linux.tar.gz tar xvf blast ia32-linux.tar 11
12 blastall formatdb bl2seq fastacmd blastpgp rpsblast blastclust.ncbirc [NCBI] DATA=[ ]/data [BLAST] BLASTDB=[ ].ncbirc [NCBI] DATA=/auto/home/is/takawaba/tool/blast02Jan18/data [BLAST] BLASTDB=/auto/home/is/takawaba/BLASTDB 12
![ncbirc [NCBI] DATA=[ ]/data [BLAST] BLASTDB=[ ].](/docs-images/47/20505917/images/page_12.jpg "ncbirc [NCBI]")
13 ftp.ncbi.nlm.nih.gov anonymous tp://ftp.ncbi.nlm.nih.gov blast/db nr nt.00.tar.gz, nt.01.tar.gz, nt.02.tar.gz nr nr.tar.gz swissprot swissprot.tar.gz pdbaa pdbaa.tar.gz gunzip formatdb 13
14 formatdb -i [ ] p F -o T formatdb -i [ ] -p T -o T -p [Program Name] blastn blastp blastx tblastn tblastx 14
![-p [Program Name] blastn](/docs-images/47/20505917/images/page_14.jpg "blastp blastx tblastn")
15 -i [Query File] -d[database] -o [Output File](Optional) blastall -p blastn -i qdna -d nt -o resultfile blastall -p blastp -i qprotein -d nr -o resultfile 15
16 -e [E-value] -F LEKHLRTYWEDFSTSSTSSSTSSTSSSTSGHRYSEKG LEKHLRTYWEDFxxxxxxxxxxxxxxxxxGHRYSEKG -m [0 or 1 or 2 or 3 or 4 or 5 or 6 or 7 or 8or 9 or 10 or 11] 0 0 -m 0 : pairwise -m 1 : query-anchored showing identities -m 2 : query-anchored no identities -m 3 : flat query-anchored, show identities -m 4 : flat query-anchored, no identities -m 5 : query-anchored no identities and blunt ends -m 6 : flat query-anchored, no identies and blunt ends -m 7 : XML Blast output -m 8 : tabular -m 9 : tabular ith comment lines -m 10: ASN,text -m 11: ASN,binary -m 4 -m 4 16
17 QUERY 1 AAIVKLGGDDGSLAFVPNNITVGAGESIEFINNAGFPHNIVFDEDAVPA-GVD--ADAI- 56 7pcy-1 AAIVKLGGDDGSLAFVPNNITVGAGESIEFINNAGFPHNIVFDEDAVPA-GVD--ADAI- 56 1iuz-1 AqIVKLGGDDGSLAFVPSKISVAAGEAIEFVNNAGFPHNIVFDEDAVPA-GVD--ADAI- 56 2plt-2 AtVKLGADSGALeFVPKTLTIkSGETVNFVNNAGFPHNIVFDEDAIPS-GVN--ADAI- 56 1pla-1 AeVKLGSDDGGLVFsPSSFTVAAGEKItFkNNAGFPHNIVFDEDeVPA-GVN--AEkI- 55 1ag6-3 VlLGGDDGSLAFLPGDFSVASGEEIvFkNNAGFPHNVVFDEDeIPS-GVD--AakIs 56 1plc-3 VlLGADDGSLAFVPSEFSISpGEKIvFkNNAGFPHNIVFDEDSIPS-GVD--ASkIs 56 9pcy-3 VlLGSgDGSLVFVPSEFSVpSGEKIvFkNNAGFPHNVVFDEDeIPA-GVD--AvkI- 55 1bypA1 AeVlLGSSDGGLAFVPSDLSIASGEKItFkNNAGFPHNdLFDKkeVPA-GVD--VtkI- 55 1pcs-3 AtVKMGSDSGALVFePSTVTIkAGEEVKWVNNklsPHNIVFDaDGVPA-dT---AakL- 56 1b3iA5 IKMGtDkyAplYePKaLSISAGDTVEFVmNkvgPHNVIFDK--VPA-GeS--ApAL- 55 1bxvA5 IKMGADNGmLAFePSTIeIqAGDTVQWVNNklaPHNVVvE g--qpeL- 49 1bawA5 VKMGADSGlLqFePaNVTVhpGDTVKWVNNklpPHNILFDDkqVPG-AskelADkL- 59 1kdj-1 AkVEVGdEvGNFkFyPDSITVSAGEAVEFtlvGetgHNIVFDipAgap-GTv--ASeL- 55 1fa4A5 VKLGSDkGlLVFePaKLTIkpGDTVEFLNNkvpPHNVVFDaalnPAkSADl-AkSL- 59 -m 4 -m 8 Excel [Query id], [Subject id], [% identity], [alignmentlength], [mismatch], [gap_opennings], [q.start], [q.end], [s.start], [s.end], [e-value], [bit score] 7pcy- 7pcy e pcy- 1iuz e pcy- 2plt e pcy- 1pla e pcy- 1ag e pcy- 1plc e pcy- 9pcy e pcy- 1bypA e pcy- 1pcs e pcy- 1b3iA e pcy- 1bxvA e pcy- 1bawA e pcy- 1kdj e pcy- 1fa4A e m 8 17
18 bl2seq : blastall bl2seq blastall -p -i -j qprotein1 qprotein2 bl2seq -p blastp -i qprotein1 j qprotein2 -o resultfile fastacmd : Blastall clustalw Fastacmd -d -s FASTA > swissprot RECA_ECOLI fastacmd d swissprot -s RECA_ECOLI RECA_ECOLI RECA_BACSU fastacmd d swissprot -s RECA_ECOLI,RECA_BACSU formatdb Parse o T 18
19 Ian Korf, Mark Yandell, Joseph Bedell BLAST. Oreilly & Associates, BLASTWEB BLAST Information Page 19
PowerPoint プレゼンテーション
解 析 の 実 践 (blast mapping assemble) 検 索 前 の 準 備 1. gw.ddbj.nig.ac.jpにログイン ssh [user name]@gw..ddbj.nig.ac.jp 2. 解 析 ノードにログイン qlogin 3. Pathの 設 定 emacs ~/.bashrc PATH= $PATH :/usr/local/bin:/usr/local/pkg/bowtie2/currentという
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Unix Unix! grep! sed! sort! cut! join! awk! (grep)! grep ' ' [...]! grep 'GO' 1433B_HUMAN.sprot!! 1433B_HUMAN.sprot GO grep '^FT' 1433B_HUMAN.sprot!! 1433B_HUMAN.sprot FT! grep -v! grep -i! grep -w!!!
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