Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
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! style="border-style: solid; border-width: 0 1px 1px 0"| Method |
! style="border-style: solid; border-width: 0 1px 1px 0"| Method |
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| + | ! style="border-style: solid; border-width: 0 1px 1px 0"| Parameter |
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! style="border-style: solid; border-width: 0 1px 1px 0"| Time |
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| style="border-style: solid; border-width: 0 1px 1px 0"| Blast v = 700 |
| style="border-style: solid; border-width: 0 1px 1px 0"| Blast v = 700 |
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| − | | style="border-style: solid; border-width: 0 1px 1px 0"| |
+ | | style="border-style: solid; border-width: 0 1px 1px 0"| b = 700, v = 700 |
| + | | style="border-style: solid; border-width: 0 1px 1px 0"| 1m53.944s |
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| − | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
+ | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
| + | | style="border-style: solid; border-width: 0 1px 1px 0"| default |
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| style="border-style: solid; border-width: 0 1px 1px 0"| 2m24.603s |
| style="border-style: solid; border-width: 0 1px 1px 0"| 2m24.603s |
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| − | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
+ | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
| + | | style="border-style: solid; border-width: 0 1px 1px 0"| n = 8 |
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| style="border-style: solid; border-width: 0 1px 1px 0"| 14m33.989s |
| style="border-style: solid; border-width: 0 1px 1px 0"| 14m33.989s |
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Revision as of 19:32, 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
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 |
