Sequence-based mutation analysis TSD Journal

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 -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>