Difference between revisions of "Tastk 2: Alignments"

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== Sequence Searches ==
 
== Sequence Searches ==
TODO:
 
what blast parameters should be used?
 
   
 
Blast:<br>
 
Blast:<br>
blastall -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/pracstrucfunc13/data/big/big_80 -O /mnt/home/student/betza/task2/hfe_blast.txt -p blastp
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blastall -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/pracstrucfunc13/data/big/big_80 -O /mnt/home/student/betza/task2/hfe_blast.txt -p blastp -v 1000
   
 
HHblits parameter:<br>
 
HHblits parameter:<br>
hhblits -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/rost_db/data/hhblits/uniprot20_02Sep11 -o /mnt/home/student/betza/task2/hfe.hhr -oa3m /mnt/home/student/betza/task2/hfe.a3m -oalis /mnt/home/student/betza/task2/hfe -ohhm /mnt/home/student/betza/task2/hfe.hhm
+
hhblits -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/rost_db/data/hhblits/uniprot20_02Sep11 -o /mnt/home/student/betza/task2/hfe.hhr -oa3m /mnt/home/student/betza/task2/hfe.a3m -oalis /mnt/home/student/betza/task2/hfe -ohhm /mnt/home/student/betza/task2/hfe.hhm -Z 1000
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increase number of lines in summary hit list to 1000 in blast and HHblits.

Latest revision as of 23:39, 3 May 2013

Sequence Searches

Blast:
blastall -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/pracstrucfunc13/data/big/big_80 -O /mnt/home/student/betza/task2/hfe_blast.txt -p blastp -v 1000

HHblits parameter:
hhblits -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/rost_db/data/hhblits/uniprot20_02Sep11 -o /mnt/home/student/betza/task2/hfe.hhr -oa3m /mnt/home/student/betza/task2/hfe.a3m -oalis /mnt/home/student/betza/task2/hfe -ohhm /mnt/home/student/betza/task2/hfe.hhm -Z 1000


increase number of lines in summary hit list to 1000 in blast and HHblits.