Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"

From Bioinformatikpedia
(Time)
(Blast)
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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 -b 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 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
   
 
==== HHblits / HHsearch ====
 
==== HHblits / HHsearch ====

Revision as of 18:32, 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 2 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