Vorlesung Einführung in die Bioinformatik - U. Scholz & M. Lange Folie #3z-1 Praktisch BLASTen & BLAST-Outputs praktisch BLASTen & BLAST-Outputs

Vorlesung Einführung in die Bioinformatik - U. Scholz & M. Lange Folie #3z-1Praktisch BLASTen & BLAST-Outputs

praktisch BLASTen praktisch BLASTen & &

BLAST-OutputsBLAST-Outputs


Ein praktisches BeispielEin praktisches Beispiel

ATGCTGTGGCAGCGTGCAGTCCAGTCTCGTACTGCAT NRPEP

1.506 kartierteGersten-Gene

2.869.704annotierteProteine

BlastXErgebnis:905 Annotation

Laufzeit:17,5 h


Lösung: Verteilung der Analysen Lösung: Verteilung der Analysen

NRPEP

NRPEP

NRPEP

NRPEP

NRPEP

...ATGCGTACGTAACCACGTAACAGTCGTCAACACAGATACGTCTGGCC

ATGCGTACGTAACCACGTAACAGTCGTCAACACAGATACGTCTGGCC




GTAGCTACGTAACCCGTAAAAGTCGTCAAAACAGATACCGTCTGGCC

GGTGCGTACGAACCCACGTAACAGTCGTTAAACAGATACAGTCTGGC

TTACGGCGTACGTAACCACGTAACAGTCGTCAACACAGATACGTCT

‚CCCATGCGTACGTAACCACGTAACAGTCGTCAACACAGATACGTCT

...


IPK Cluster BROCKEN IPK Cluster BROCKEN

Ergebnis:905 Annotation

72 Nodes ->Laufzeit:16 min


CEF: Cluster Execution FrameworkCEF: Cluster Execution Framework#!/bin/bashprojdir=/data/pdw-16/agbi/projects/#split query filepython2.3 /data/pdw-20/python_scripts/splitFas2.py -i Clones.fasta -o

$projdir -n 500blast_db=$projdir/wheat_consensus.txtmergescript=$projdir/domerge.shecho "#!/bin/sh" > $mergescriptecho "cat \\" >> $mergescriptz=0for i in split/*doscript_file=$projdir/script/blastjob_$$_$z.shresult_file=$projdir/result/blastresult_$$_$z.txtlog_file=$projdir/log/joblog_$$_$zecho "#!/bin/sh" > $script_file#echo "cd $projdir" >> $script_fileecho "/usr/bin/blastall -i $projdir/$i -p blastn -d $blast_db -m0 -e 1E-10

-v 10 -b 10 -o $result_file" >> $script_fileecho "$result_file \\" >> $mergescriptqsub -o $log_file.out -e $log_file.err -q long $script_fileecho "qsub -o $log_file.out -e $log_file.err -q long $script_file"z=`expr $z + 1`doneecho ">final_result.txt" >> $mergescriptecho "rm log/* script/* " >> $mergescript

file server/data/pdw-16/

file server/data/pdw-20/

Metadata about Tools (NCBI BLAST, Spidey, …) Tool parameters (-i FASTA-query, …) Files (FASTA, blastable, …) Jobs/sub jobs (progress, finished, …)

…

master/head node pdw-22

22 nodes

CEF GUI CEF SOAPWeb Services


CEF: APEX GUI CEF: APEX GUI


Eingabe EST-SequenzEingabe EST-Sequenz

>HY01A03T GAATTCGGCACCAGAGTGAGCACGCAAGCCAGTGTTTGTAGCCAGCAGCCACAATGGCCGGGAACATGCT AGCCAACTATGTCCAAGTCTACGTCATGCTCCCGCTGGATGTCGTGAGCGTCGACAACAAGTTCGAGAAG GGCGACGAGATCAGGGCGCAGCTGAAGAAGCTGACGGAGGCTGGCGTGGACGGCGTCATGATAGACGTCT GGTGGGGGCTGGTGGAGGGCAAGGGCCCCAAGGCCTACGACTGGAGCGCCTACAAGCAGGTCTTCGACCT GGTGCACGAGGCCAGGCTCAAGCTGCAGGCCATCATGTCGTTCCACCAGTGCGGTGGCAACGTCGGCGAC GTAGTCAACATCCCCATCCCACAGTGGGTGCGGGATGTCGGCGCTACCGACCCCGACATTTTCTACACGA ACCGCAGAGGGACGAGGAACATCGAGTACCTCACCCTTGGAGTGGATGACCAACCTCTCTTCCATGGAAG AACTGCCGTCCAGATGTATCATGATTACATGGCGAGCTTCAGGGAAAACATGAAAAAGTTCTTGGATGCC GGTACCATCGTGGACATTGAAGTGGGACTTGGCCCGGCTGGAGAGATGAGGTACCCATCCTATCCTCAGA GCCAGGGATGGGTCTTCCCAGGCATCGGAGAATTCATCTGCTATGATAAGTACCTGGAAGCAGACTTCAA


BlastN-ResultatBlastN-Resultat>HY01A03T Length = 700 Plus Strand HSPs: Score = 2595 (395.4 bits), Expect = 3.0e-112, P = 3.0e-112 Identities = 573/618 (92%), Positives = 573/618 (92%), Strand = Plus / PlusQuery: 77 CTATGTCCAAGTCTACGTCATGCTCCCGCTGGATGTCGTGAGC--GT-CGACAACAAGTT 133 ||| ||| | | || | | | | || || |||| | | || ||| || Sbjct: 89 CTACGTC-ATG-CTCCCGCTGGATGTCG-TGAGCGTCGACAACAAGTTCGAGAAGGGCGA 145Query: 134 CGAGA--AGGGCGACGAGATCAGGAAGCTGACGGAGGCTGGCGTGGACGGCGTCATGATA 191 ||||| |||||| | || | | |||||||||||||||||||||||||||||||||||||Sbjct: 146 CGAGATCAGGGCG-C-AGCTGAAGAAGCTGACGGAGGCTGGCGTGGACGGCGTCATGATA 203Query: 192 GACGTCTGGTGGGGGCTGGTGGAGGGCAAGGGCCCCAAGGCCTACGACTGGAGCGCCTAC 251 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||Sbjct: 204 GACGTCTGGTGGGGGCTGGTGGAGGGCAAGGGCCCCAAGGCCTACGACTGGAGCGCCTAC 263Query: 252 AAGCAGGTCTTCGACCTGGTACACGAGGCCAGGCTCAAGCTGCAGGCCATCATGTCGTTC 311 |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||Sbjct: 264 AAGCAGGTCTTCGACCTGGTGCACGAGGCCAGGCTCAAGCTGCAGGCCATCATGTCGTTC 323Query: 312 CACCCCGTGCGGTGGCAACGTCGGCGACGTAGTCAACATCCCCATCCCACAGTGGGTGCG 371 |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||Sbjct: 324 CACCA-GTGCGGTGGCAACGTCGGCGACGTAGTCAACATCCCCATCCCACAGTGGGTGCG 382Query: 372 GGATGTCGGCGCTACCGACCCCGACATTTTCCACACGAACCTCAGAGGGACGAGGAACAT 431 ||||||||||||||||||||||||||||||| ||||||||| ||||||||||||||||||Sbjct: 383 GGATGTCGGCGCTACCGACCCCGACATTTTCTACACGAACCGCAGAGGGACGAGGAACAT 442Query: 432 CGAGTACCTCACCCTTGGAGTGGATGACCAACCTCTCTTCCATGGAAGAACTGCCGTCCA 491 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||Sbjct: 443 CGAGTACCTCACCCTTGGAGTGGATGACCAACCTCTCTTCCATGGAAGAACTGCCGTCCA 502Query: 492 GATGTATCATGATTACATGGCGAGCTTCAGGGAAAACATGAAAAAGTTCTTGGATGCCGG 551 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||Sbjct: 503 GATGTATCATGATTACATGGCGAGCTTCAGGGAAAACATGAAAAAGTTCTTGGATGCCGG 562Query: 552 TACCATCGTGGACA---A-GTGGGACTTGGCCCGGCTGGAGAGATGAGGTACCCATCCTA 607 |||||||||||||| | |||||||||||||||||||||||||||||||||||||||||Sbjct: 563 TACCATCGTGGACATTGAAGTGGGACTTGGCCCGGCTGGAGAGATGAGGTACCCATCCTA 622Query: 608 TCCTCAGAGCCAGGGATGGGTCTTCCCAGGCATCGGAGAATTCATCTGCTATGATAAGTA 667 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||Sbjct: 623 TCCTCAGAGCCAGGGATGGGTCTTCCCAGGCATCGGAGAATTCATCTGCTATGATAAGTA 682Query: 668 CCTGGAAGCAGACTTCAA 685 ||||||||||||||||||Sbjct: 683 CCTGGAAGCAGACTTCAA 700


BlastX-ResultatBlastX-Resultat

>dbj|BAC83773.1| Gene info putative beta-amylase [Oryza sativa (japonica cultivar-group)] gb|EAZ40178.1| hypothetical protein OsJ_023661 [Oryza sativa (japonica cultivar-group)]Length=488

Score = 403 bits (1036), Expect = 4e-111 Identities = 191/215 (88%), Positives = 200/215 (93%), Gaps = 0/215 (0%) Frame = +3

Query 54 MAGNMLANYVQVYVMLPLDVVSVDNKFEKGDEIRAQLKKLTEAGVDGVMIDVWWGLVEGK 233 MAGN+LANYVQV VMLPLDVV+VDNKFEK DE RAQLKKLTEAGVDGVM+DVWWGLVEGKSbjct 1 MAGNLLANYVQVNVMLPLDVVTVDNKFEKVDETRAQLKKLTEAGVDGVMVDVWWGLVEGK 60

Query 234 GPKAYDWSAYKQVFDLVHEARLKLQAIMSFHQCGGNVGDVVNIPIPQWVRDVGATDPDIF 413 GP +YDW AYKQ+F LV EA LKLQAIMSFHQCGGNVGD+VNIPIPQWVRDVGA+DPDIFSbjct 61 GPGSYDWEAYKQLFRLVQEAGLKLQAIMSFHQCGGNVGDIVNIPIPQWVRDVGASDPDIF 120

Query 414 YTNRRGTRNIEYLTLGVDDQPLFHGRTAVQMYHDYMASFRENMKKFLDAGTIVDIEVGLG 593 YTNR G RNIEYLTLGVDDQPLFHGRTA+QMY DYM SFRENM +FLD G IVDIEVGLGSbjct 121 YTNRGGARNIEYLTLGVDDQPLFHGRTAIQMYADYMKSFRENMAEFLDTGVIVDIEVGLG 180

Query 594 PAGEMRYPSYPQSQGWVFPGIGEFICYDKYLEADF 698 PAGEMRYPSYPQSQGWVFPGIGEFICYDKYLEADFSbjct 181 PAGEMRYPSYPQSQGWVFPGIGEFICYDKYLEADF 215

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Vorlesung Einführung in die Bioinformatik - U. Scholz & M. Lange Folie #3z-1 Praktisch BLASTen & BLAST-Outputs praktisch BLASTen & BLAST-Outputs