cDNA Vector trim.

[David Martin]

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