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

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m (= Sequence searches)
(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</code>
 
<code>blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P06280.fasta -m 0 -o blastsearch_default.out -v 700</code>
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The run took about 1.5 minutes[http://www.example.com link title].
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==== HHblits / HHsearch ====
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We searched the "big80" database with HHblits with the following command:
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<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>
   
 
== Time ==
 
== Time ==

Revision as of 12:56, 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 minuteslink title.

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

Time

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