Re: Debian software which allows searching nucleotide / amino acid sequence and showing intron/exon boundries or begin/termination of translations
On Thu, Jun 30, 2005 at 04:52:32PM -0400, Aaron M. Ucko wrote:
> Mark Farnell <mark.farnell@gmail.com> writes:
>
> > One can use pubmed nucleotide easily for searching DNA sequences for a
> > particular gene. However is there any website / debian software which
> > also shows other information such as intron/exon boundaries, beginning
> > / end of transcriptions? For aa sequences, to show the boundries of
> > exons.
>
> Have you tried sequin, in the ncbi-tools-x11 package?
>
> > Also, is there any Debian program which can automate design of primers
> > for different purposes?
>
> Not sure about this one, but the ncbi-epcr package will let you
> simulate the effects of given primers on a given sequence.
primer-perl helps with primer design. I have it on my private repository
http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/
Cheers,
Steffen
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