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

From Bioinformatikpedia
(Sequence searches)
(Time)
Line 29: Line 29:
 
| style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits default
 
| style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits default
 
| style="border-style: solid; border-width: 0 1px 1px 0"| 2m24.603s
 
| style="border-style: solid; border-width: 0 1px 1px 0"| 2m24.603s
  +
|-
  +
| style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits n = 8
  +
| style="border-style: solid; border-width: 0 1px 1px 0"| 14m33.989s
 
|}
 
|}

Revision as of 13:15, 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 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

Method Time
Blast v = 700 1m30.985s
HHBlits default 2m24.603s
HHBlits n = 8 14m33.989s