Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
Rackersederj (talk | contribs) (→Time) |
Rackersederj (talk | contribs) (→Blast) |
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We searched the "big80" database with Blast with the following command: |
We searched the "big80" database with Blast with the following command: |
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− | <code>blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P06280.fasta -m 0 -o blastsearch_default.out -v 700</code> |
+ | <code>blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P06280.fasta -m 0 -o blastsearch_default.out -v 700 -b 700</code> |
The run took about 1.5 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]) |
The run took about 1.5 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]) |
Revision as of 19:30, 24 April 2012
Sequence searches
Blast
We searched the "big80" database with Blast with the following command:
blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P06280.fasta -m 0 -o blastsearch_default.out -v 700 -b 700
The run took about 1.5 minutes (see section Time)
HHblits / HHsearch
We searched the "big80" database with HHblits with the following command:
hhblits -i ~/Desktop/P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003
The run took about 2.5 minutes (see section Time)
Also, we ran HHblits with 8 iterations, instead of the preset 2. This took 14.5 minutes.
hhblits -i ~/Desktop/P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default_n8.out -E 0.003 -n 8
Time
Method | Time |
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Blast v = 700 | 1m30.985s |
HHBlits default | 2m24.603s |
HHBlits n = 8 | 14m33.989s |