Difference between revisions of "Sequence-based mutation analysis TSD Journal"

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m (Substitution matrices)
m (Substitution matrices)
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PSI-Blast was called as follows, using the parameters from Task 2, if note already given by the Task description (number of iterations):
 
PSI-Blast was called as follows, using the parameters from Task 2, if note already given by the Task description (number of iterations):
 
<source lang="bash">
 
<source lang="bash">
  +
wget http://www.uniprot.org/uniprot/P06865.fasta
 
PAT=`pwd`
 
PAT=`pwd`
 
blastpgp -m 8 -C $PAT/blastpgp_pssm -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 -j 5 > $PAT/lastpgp.out
 
blastpgp -m 8 -C $PAT/blastpgp_pssm -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 -j 5 > $PAT/lastpgp.out

Revision as of 20:53, 14 June 2012

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To improve on the readability of the journal, only the basic steps and program calls are outlined here, while the full source code is linked to like this.

Substitution matrices

Quantiles can be easily calculated in R, using <source lang="bash"> quantile(m) #Where m is a matrix </source>

PSI-Blast was called as follows, using the parameters from Task 2, if note already given by the Task description (number of iterations): <source lang="bash"> wget http://www.uniprot.org/uniprot/P06865.fasta PAT=`pwd` blastpgp -m 8 -C $PAT/blastpgp_pssm -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 -j 5 > $PAT/lastpgp.out </source>