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

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(Blast)
(Sequence searches)
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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>
 
<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>
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The run took about 2.5 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
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Also, we ran HHblits with 8 iterations, instead of the preset 2. This took .
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<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>
   
 
== Time ==
 
== Time ==

Revision as of 13:04, 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 .

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