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 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.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j2_10000.out

real	3m21.031s
user	2m44.750s
sys	0m10.270s


time blastpgp -C $TSK/h002j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j10_10000.out

real	16m39.699s
user	14m22.150s
sys	0m41.310s


time blastpgp -C $TSK/h1e-10j2.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j2_10000.out

real	3m6.093s
user	2m48.260s
sys	0m6.020s


time blastpgp -C $TSK/h1e-10j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j10_10000.out

real	16m41.797s
user	15m18.350s
sys	0m28.890s


time blastpgp -R $TSK/h002j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j2_100000.out

real	28m17.459s
user	18m26.930s
sys	2m46.200s


time blastpgp -R $TSK/h002j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j10_100000.out

real	367m15.021s (srsly...)
user	310m31.210s
sys	14m39.460s
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed with idx 2048" messages


time blastpgp -R $TSK/h1e-10j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j2_100000.out

real	26m43.350s
user	19m54.380s
sys	2m3.900s


time blastpgp -R $TSK/h1e-10j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j10_100000.out

real	64m4.575s
user	47m16.970s
sys	4m54.890s
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed with idx 2048" messages

HHblits

TSK="/mnt/home/student/bernhoferm/task2"
HHB="/mnt/project/pracstrucfunc12/data/hhblits"


time hhblits -d $HHB/uniprot20_current -i $TSK/Q30201.fasta -Z 600 -B 600 -o $TSK/align2/hhblits_default_600.out

real	13m13.813s
user	5m4.400s
sys	2m45.520s

MSA

#!/bin/bash
time t_coffee /mnt/home/student/joerdensv/newGroups/group0-40.fasta -output=fasta_aln
time t_coffee /mnt/home/student/joerdensv/newGroups/group0-99.fasta -output=fasta_aln
time t_coffee /mnt/home/student/joerdensv/newGroups/group60-99.fasta -output=fasta_aln
time muscle -in /mnt/home/student/joerdensv/newGroups/group60-99.fasta -out group60-99muscle.fasta -quiet
time muscle -in /mnt/home/student/joerdensv/newGroups/group0-99.fasta -out group0-99muscle.fasta -quiet
time muscle -in /mnt/home/student/joerdensv/newGroups/group0-40.fasta -out group0-40muscle.fasta -quiet
time clustalw -align -infile=/mnt/home/student/joerdensv/newGroups/group60-99.fasta -outfile=/mnt/home/student/joerdensv/newGroups/group60-99clustalw.fasta -output=fasta
time clustalw -align -infile=/mnt/home/student/joerdensv/newGroups/group0-99.fasta -outfile=/mnt/home/student/joerdensv/newGroups/group0-99clustalw.fasta -output=fasta
time clustalw -align -infile=/mnt/home/student/joerdensv/newGroups/group0-40.fasta -outfile=/mnt/home/student/joerdensv/newGroups/group0-40clustalw.fasta -output=fasta