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

Revision as of 14:14, 24 April 2012

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)

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

Method	Time
Blast v = 700	1m30.985s
HHBlits default	2m24.603s

@@ Line 14: / Line 14: @@
 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 .
+Also, we ran HHblits with 8 iterations, instead of the preset 2. This took 14.5 minutes.
 <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>