Difference between revisions of "Task2 Hemochromatosis Protocol"
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Bernhoferm (talk | contribs) (→HHblits) |
Bernhoferm (talk | contribs) (→HHblits) |
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=== HHblits === |
=== HHblits === |
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TSK="/mnt/home/student/bernhoferm/task2" |
TSK="/mnt/home/student/bernhoferm/task2" |
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| − | BIG="/mnt/project/pracstrucfunc12/data/big" |
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time hhblits -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -i $TSK/Q30201.fasta -Z 600 -B 600 -o $TSK/align/hhblits_default_600.out |
time hhblits -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -i $TSK/Q30201.fasta -Z 600 -B 600 -o $TSK/align/hhblits_default_600.out |
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Revision as of 22:05, 5 May 2012
Sequence Searches
Blast
TSK="/mnt/home/student/bernhoferm/task2" BIG="/mnt/project/pracstrucfunc12/data/big" time blastall -p blastp -d $BIG/big_80 -i $TSK/Q30201.fasta -b 1250 -v 1250 -o $TSK/align/blast_default_1250.out real 1m8.589s user 1m6.810s sys 0m1.110s
PSI-Blast
TSK="/mnt/home/student/bernhoferm/task2" BIG="/mnt/project/pracstrucfunc12/data/big" time blastpgp -C $TSK/h002j2.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 1250 -v 1250 -o $TSK/align/blastpgp_h0.002_j2_1250.out real 3m2.887s user 2m38.360s sys 0m5.900s time blastpgp -C $TSK/h002j10.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 1250 -v 1250 -o $TSK/align/blastpgp_h0.002_j10_1250.out real 14m9.579s user 13m22.190s sys 0m16.200s time blastpgp -C $TSK/h10e-10j2.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 10e-10 -j 2 -b 1250 -v 1250 -o $TSK/align/blastpgp_h10e-10_j2_1250.out real 2m42.516s user 2m38.380s sys 0m2.540s time blastpgp -C $TSK/h10e-10j10.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 10e-10 -j 10 -b 1250 -v 1250 -o $TSK/align/blastpgp_h10e-10_j10_1250.out real 11m23.359s user 11m11.340s sys 0m8.770s
HHblits
TSK="/mnt/home/student/bernhoferm/task2" time hhblits -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -i $TSK/Q30201.fasta -Z 600 -B 600 -o $TSK/align/hhblits_default_600.out real 20m46.643s user 5m41.040s sys 2m43.670s
