Task2 Hemochromatosis Protocol

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"
BIG="/mnt/project/pracstrucfunc12/data/big"

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