Difference between revisions of "Task2 Hemochromatosis Protocol"
From Bioinformatikpedia
Bernhoferm (talk | contribs) (→Sequence Searches) |
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user 5m4.400s |
user 5m4.400s |
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sys 2m45.520s |
sys 2m45.520s |
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| − | == Scripts == |
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== MSA == |
== MSA == |
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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/group0-99.fasta -outfile=/mnt/home/student/joerdensv/newGroups/group0-99clustalw.fasta -output=fasta |
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time clustalw -align -infile=/mnt/home/student/joerdensv/newGroups/group0-40.fasta -outfile=/mnt/home/student/joerdensv/newGroups/group0-40clustalw.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 |
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| + | == Scripts == |
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Revision as of 15:40, 7 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.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
