Difference between revisions of "Sequence-based mutation analysis TSD Journal"
From Bioinformatikpedia
m |
m (→Substitution matrices) |
||
| Line 13: | Line 13: | ||
wget http://www.uniprot.org/uniprot/P06865.fasta |
wget http://www.uniprot.org/uniprot/P06865.fasta |
||
PAT=`pwd` |
PAT=`pwd` |
||
| − | blastpgp -m 8 - |
+ | blastpgp -m 8 -Q $PAT/blastpgp_pssm -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 -j 5 > $PAT/lastpgp.out |
</source> |
</source> |
||
Revision as of 01:37, 15 June 2012
Back to results.
To improve on the readability of the journal, only the basic steps and program calls are outlined here, while the full source code of self-written scripts 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 -Q $PAT/blastpgp_pssm -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 -j 5 > $PAT/lastpgp.out </source>
