Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
From Bioinformatikpedia
Rackersederj (talk | contribs) (→Blast) |
Rackersederj (talk | contribs) (→Sequence searches) |
||
Line 11: | Line 11: | ||
<code>hhblits -i ~/Desktop/P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003</code> |
<code>hhblits -i ~/Desktop/P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003</code> |
||
+ | |||
+ | The run took about 2.5 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]) |
||
+ | |||
+ | Also, we ran HHblits with 8 iterations, instead of the preset 2. This took . |
||
+ | |||
+ | <code>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</code> |
||
== Time == |
== Time == |
Revision as of 14:04, 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
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 .
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 |
---|---|
Blast v = 700 | 1m30.985s |
HHBlits default | 2m24.603s |