[EMBOSS] Does emboss have a handy way for mutate a protein sequence
Zhiqiang Ye
yezhiqiang at gmail.com
Tue Mar 7 16:42:00 UTC 2006
hi, Guy Bottu
Thank you. But I have to do a batch of these subsitituion, so a
command line solution will be better. I write an ugly shell script to
do this according to David Bauer.
#!/bin/sh
mutation=$2;
WT=${mutation:0:1};
POS=${mutation:1:${#mutation}-2};
MT=${mutation: -1}
POS2=`expr $POS - 1`
cat $1 | cutseq -filter -from $POS -to $POS | pasteseq -filter -pos
$POS2 -bs asis:$MT | descseq -filter -append -desc " (mutant:
$mutation )"
With this script mutate.sh in my ~/bin, I can type this:
mutate.sh foo.fasta A2L
Best
--
Zhiqiang Ye
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