Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
Staniewski (talk | contribs) (→Sequence searches) |
Staniewski (talk | contribs) (→Psi-Blast) |
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=== Psi-Blast === |
=== Psi-Blast === |
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+ | Iterations: 2 |
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+ | Evalue: 0.002 |
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+ | |||
+ | real 3m30.256s |
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+ | user 2m58.070s |
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+ | sys 0m13.360s |
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+ | |||
+ | Iterations: 2 |
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+ | Evalue: 0.000000001 |
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+ | |||
+ | real 3m8.507s |
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+ | user 3m5.180s |
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+ | sys 0m2.400s |
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+ | |||
+ | Iterations: 2 |
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+ | Evalue: 0.0000000001 |
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+ | |||
+ | real 3m10.271s |
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+ | user 3m7.620s |
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+ | sys 0m2.190s |
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+ | |||
+ | Iterations: 10 |
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+ | Evalue: 0.002 |
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+ | |||
+ | real 15m29.218s |
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+ | user 15m8.910s |
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+ | sys 0m12.730s |
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+ | |||
+ | Iterations: 10 |
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+ | Evalue: 0.000000001 |
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+ | |||
+ | real 16m33.748s |
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+ | user 16m12.500s |
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+ | sys 0m13.080s |
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+ | |||
+ | Iterations: 10 |
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+ | Evalue: 0.0000000001 |
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+ | |||
+ | real 16m20.137s |
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+ | user 15m55.910s |
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+ | sys 0m13.190s |
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=== HHblits / HHsearch === |
=== HHblits / HHsearch === |
Revision as of 18:37, 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
Iterations: 2 Evalue: 0.002 real 3m30.256s user 2m58.070s sys 0m13.360s Iterations: 2 Evalue: 0.000000001 real 3m8.507s user 3m5.180s sys 0m2.400s Iterations: 2 Evalue: 0.0000000001 real 3m10.271s user 3m7.620s sys 0m2.190s Iterations: 10 Evalue: 0.002 real 15m29.218s user 15m8.910s sys 0m12.730s Iterations: 10 Evalue: 0.000000001 real 16m33.748s user 16m12.500s sys 0m13.080s Iterations: 10 Evalue: 0.0000000001 real 16m20.137s user 15m55.910s sys 0m13.190s
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 |
---|---|---|
Blast v = 700 | b = 700, v = 700 | 1m53.944s |
HHBlits | default | 2m24.603s |
HHBlits | n = 8 | 14m33.989s |