Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
Rackersederj (talk | contribs) (→Blast) |
Staniewski (talk | contribs) (→Sequence searches) |
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== Sequence searches == |
== Sequence searches == |
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− | + | === 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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The run took about 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]) |
The run took about 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]) |
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− | + | === Psi-Blast === |
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+ | === HHblits / HHsearch === |
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We searched the "big80" database with HHblits with the following command: |
We searched the "big80" database with HHblits with the following command: |
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Revision as of 18:33, 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 2 minutes (see section Time)
Psi-Blast
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
We evaluated the time the programs ran with the command "time"
Method | Parameter | Time |
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Blast v = 700 | b = 700, v = 700 | 1m53.944s |
HHBlits | default | 2m24.603s |
HHBlits | n = 8 | 14m33.989s |