[EMBOSS] pasteseq

[ajb at ebi.ac.uk]

Alternatively you might be able to use 'biosed'. That program will
replace all occurrences of a sequence string with a replacement
string. As it replaces all occurrences you need to be careful about
uniqueness. So, if your sequence file (myseq.seq) was:

>MYSEQ
ACDEFGHI

You could use the following to insert a gap at the start:

   biosed -target "ACDE" -replace "-ACDE" myseq.seq

Alan


> Hi,
>
> I'm an EMBOSS newbie but have a simple question. For the pasteseq
> program I'm trying to paste in the character '-' into my sequence:
>
>> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa
>
> But my sequence is unchanged after I run the above command. However if
> I change insert.fa to be the sequence NN it works fine. Is there
> anyway I can insert the '-' character
>
> Much thanks,
>
> Amit Indap
> Cornell University
>
>
>
>
>
> --
> Amit Indap
> http://www.bscb.cornell.edu/Homepages/Amit_Indap/
>
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