Sequence-based mutation analysis TSD Journal

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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 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>

To create the PSSM, PSI-Blast was called as follows, using the parameters from Task 2, if not 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>