Difference between revisions of "Sequence-based mutation analysis TSD Journal"
From Bioinformatikpedia
m (#Where) |
m (→Substitution matrices) |
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<source lang="bash"> |
<source lang="bash"> |
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quantile(m) #Where m is a matrix |
quantile(m) #Where m is a matrix |
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| + | </source> |
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| + | |||
| + | PSI-Blast was called as follows, using the parameters from Task 2, if note already given by the Task description (number of iterations): |
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| + | <source lang="bash"> |
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| + | PAT=`pwd` |
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| + | 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 |
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</source> |
</source> |
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Revision as of 20:52, 14 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 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"> 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>
