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 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>