Difference between revisions of "ARSA search protocol"
From Bioinformatikpedia
m (Created page with " # Run blast: blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -i ARSA.fas > ARSA.blast # find unique matches cut -f 2 ARSA.blast | uniq >…") |
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| + | == Blast == |
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| − | # Run blast: |
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| + | # Run blast: |
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| − | blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -i ARSA.fas > ARSA.blast |
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| + | blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -i ARSA.fas > ARSA.blast |
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# find unique matches |
# find unique matches |
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cut -f 2 ARSA.blast.uniq.worseE10 > ARSA.blast.uniq.worseE10.matchIDs |
cut -f 2 ARSA.blast.uniq.worseE10 > ARSA.blast.uniq.worseE10.matchIDs |
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cut -d "|" -f 2 ARSA.blast.uniq.worseE10.matchIDs > ARSA.blast.uniq.worseE10.matchIDs.clean |
cut -d "|" -f 2 ARSA.blast.uniq.worseE10.matchIDs > ARSA.blast.uniq.worseE10.matchIDs.clean |
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| + | |||
| + | == PSI-Blast == |
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| + | |||
| + | # run PSI-Blast with different combinations of parameters |
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| + | > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 2 -i ARSA.fas -o ARSA.psiBlast.j2.hDefault |
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| + | 280.470u 30.420s 5:55.56 87.4% 0+0k 18005712+1880io 792pf+0w |
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| + | > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 10 -i ARSA.fas -o ARSA.psiBlast.j10.hDefault |
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| + | [blastpgp] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx 2048 |
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| + | 2111.750u 44.740s 36:55.25 97.3% 0+0k 12951072+11856io 1271pf+0w |
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| + | > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 2 -h 1e-10 -i ARSA.fas -o ARSA.psiBlast.j2.h1e-10 |
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| + | > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 10 -h 1e-10 -i ARSA.fas -o ARSA.psiBlast.j10.h1e-10 |
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Revision as of 13:39, 12 April 2012
Blast
# Run blast: blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -i ARSA.fas > ARSA.blast
# find unique matches cut -f 2 ARSA.blast | uniq > ARSA.blast.matchIDs.uniq uniq -w 44 ARSA.blast > ARSA.blast.uniq
# use R to plot:
# within R: histogram of log10 Evalue for blast run
blastTable = read.table("ARSA.blast.uniq")
pdf("ARSA_blastHistogram_eVal.pdf")
logeval.hist <- hist(log10(blastTable$V11), breaks=100, plot=FALSE)
plot(logeval.hist, col="blue", main="BLAST logarithm of E-values", xlab="lg(E-Value)")
dev.off()
# within R: histogram of %identity for blast run
blastTable = read.table("ARSA.blast.uniq")
pdf("ARSA_blastHistogram_id.pdf")
id.hist <- hist(blastTable$V3, breaks=5, plot=FALSE)
plot(id.hist, col="blue", main="BLAST sequence identity distribution", xlab="percent identity")
dev.off()
# create lists of Uniprot IDs for analysis for GO annotations grep -n "1e-10" ARSA.blast.uniq tail -n +1721 ARSA.blast.uniq > ARSA.blast.uniq.worseE10 cut -f 2 ARSA.blast.uniq.worseE10 > ARSA.blast.uniq.worseE10.matchIDs cut -d "|" -f 2 ARSA.blast.uniq.worseE10.matchIDs > ARSA.blast.uniq.worseE10.matchIDs.clean
PSI-Blast
# run PSI-Blast with different combinations of parameters > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 2 -i ARSA.fas -o ARSA.psiBlast.j2.hDefault 280.470u 30.420s 5:55.56 87.4% 0+0k 18005712+1880io 792pf+0w > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 10 -i ARSA.fas -o ARSA.psiBlast.j10.hDefault [blastpgp] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx 2048 2111.750u 44.740s 36:55.25 97.3% 0+0k 12951072+11856io 1271pf+0w > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 2 -h 1e-10 -i ARSA.fas -o ARSA.psiBlast.j2.h1e-10 > blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -j 10 -h 1e-10 -i ARSA.fas -o ARSA.psiBlast.j10.h1e-10
