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.
Contents
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>
Structural visualisation
Pymol, see Mutagenesis.
Prediction
PolyPhen2
PolyPhen 2 predictions were done using the webserver's batch mode. All settings were left at default values. Here are batch file and query sequence.
SIFT
SIFT predictions were performed using the webserver at default values (database: UniRef90 2011 Apr). Here is the input mutation file.
SNAP
snap2 -i P06865.fasta -o snap.output -m all --tolerate egrep "(M1|L39|C58|L127|R170|R178|S210|D258|L451|E482)[A-Z]+" snap.out > filteredsnap.out egrep "M1V|L39R|C58Y|L127R|R170W|R178H|S210F|D258H|L451V|E482K" snap.out > onlyRealSNPsnap.out
