cDNA Vector trim.

[Phillip San Miguel]

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
>
[...]

If you have the phredPhrap package already, you might find cross_match 
sufficient. Convert your phd files to a fasta and qual files using 
phd2fasta. When you do the comparsion with cross_match, a large table of 
the quality values of the mis-matches is generated. Not sure if it is 
what you are looking for. I generally am looking for ways to filter out 
this output. Help is at www.phrap.org.
Phillip SanMiguel
Purdue Genomics Core