cDNA Vector trim.

[Matthew H. Bemis]

David,
thanks for the info.  I've read up on gap4, and it does look like I'll be
using this, but I am encountering XFree86 issues on our macosx server.  I
am an avid X user, but on linux.  Using bash I export the display to the
correct name, and i try to add the local host to xauth...well I really
have been trying to just xhost + the world.
The program gap4 will not start. any ideas??


On Thu, 20 Mar 2003, David Martin wrote:

> On 20/3/03 2:47 pm, "Matthew H. Bemis" <bemis at io.iol.unh.edu> wrote:
>
> > 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!
>
> Checkout the staden package which does all sorts of things you would find
> useful, in particular pregap4 and gap4.
>
> ..d
>
> > 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
> >>
> >
>
> --
> David Martin PhD
> Bioinformatics Scientific Officer
> Post-Genomics and Molecular Interactions Centre
> University of Dundee
>