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

Revision as of 18:33, 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 -b 700

The run took about 2 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

We evaluated the time the programs ran with the command "time"

@@ Line 1: / Line 1: @@
 == Sequence searches ==
-==== Blast ====
+=== Blast ===
 We searched the "big80" database with Blast with the following command:
@@ Line 7: / Line 7: @@
 The run took about 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
-==== HHblits / HHsearch ====
+=== Psi-Blast ===
+=== HHblits / HHsearch ===
 We searched the "big80" database with HHblits with the following command: