Difference between revisions of "Task2 Hemochromatosis Protocol"
From Bioinformatikpedia
Bernhoferm (talk | contribs) (→HHblits) |
Bernhoferm (talk | contribs) (→Blast) |
||
| Line 5: | Line 5: | ||
BIG="/mnt/project/pracstrucfunc12/data/big" |
BIG="/mnt/project/pracstrucfunc12/data/big" |
||
| − | time blastall -p blastp -d $BIG/big_80 -i $TSK/Q30201.fasta -b |
+ | time blastall -p blastp -d $BIG/big_80 -i $TSK/Q30201.fasta -b 1500 -m 8 -o $TSK/align2/blast_default_1500.out |
| − | real |
+ | real 1m24.100s |
| − | user |
+ | user 1m5.950s |
| − | sys |
+ | sys 0m3.500s |
=== PSI-Blast === |
=== PSI-Blast === |
||
Revision as of 15:12, 6 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 1500 -m 8 -o $TSK/align2/blast_default_1500.out real 1m24.100s user 1m5.950s sys 0m3.500s
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
