cDNA Vector trim.

[Matthew H. Bemis]

Hi,
Thanks for the advice!  The programs work great. Now I have all this data
and I have phred( phd.1 ) files that I'd like to align and look for
mismatches( high score mismatches ).  Is there software for this?
I have four file types to work with here:
.seq
fasta
phd.1
scf
if there software out there for looking for high quality mutations?
writing software is not out of the question for me either.  I am a cs
graduate student, but I'd rather not re-invent the wheel.
thanks in advance!
Matt Bemis

On Tue, 18 Mar 2003, David Martin wrote:

> On 18/3/03 3:06 pm, "Matthew H. Bemis" <bemis at io.iol.unh.edu> wrote:
>
> > Hello,
> > I have never used emboss before, and I would like to know if there exists
> > a trimming program to cut a vector off some sequence samples I have, and
> > stop trimming at my LokI site.  I've compiled the full set of tools on a
> > new Mac OSX, and I have all of them available to me.
> > any advice would be greatly appreciated
>
> $ wossname vector
> Finds programs by keywords in their one-line documentation
> SEARCH FOR 'VECTOR'
> vectorstrip      Strips out DNA between a pair of vector sequences
>
>
> regards
>
> ..d
>
> > thanks,
> > matt bemis
> >
>
> --
> David Martin PhD
> Bioinformatics Scientific Officer
> Post-Genomics and Molecular Interactions Centre
> University of Dundee
>