[Genome] Fwd: cool part 2

[Robert Kuhn]

this mailing-list question might also be useful.
for degenerate codes, the full range of possible sequences 
would have to be included in the .fa file.


 https://www.soe.ucsc.edu/pipermail/genome/2006-May/010707.html


			--b0b kuhn


> From genome at soe.ucsc.edu  Thu Jun  7 14:28:48 2007
> To: Tim Hefferon <thefferon at mail.nih.gov>
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] Fwd: cool part 2
> 
> Good Afternoon Tim:
> 
> Thanks for refreshing this important feature request.  We realize it
> would be useful to have it behave like that.  Unfortunately it does
> not at this time.
> 
> At the current time we can only do such things off-line with the kent
> source tree utilities.
> 
> I have recently been investigating the ngrep program, along with
> the patmatch front-end, as mentioned by Max in the genome email list:
> 	http://www.soe.ucsc.edu/pipermail/genome/2007-April/013327.html
> 	http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl
> 
> --Hiram
> 
> Tim Hefferon wrote:
> > Begin forwarded message:
> > 
> >> From: Tim Hefferon <timhefferon at gmail.com>
> >> Date: April 22, 2007 9:19:05 AM GMT-06:00
> >> To: genome at soe.ucsc.edu
> >> Subject: cool part 2
> >>
> >> Hi Again,
> >>
> >> Crucial to the degenerate 'short match' feature I e-mailed about  
> >> earlier this morning would be the ability to access the data via  
> >> the Table Browser. Right now the 'short match' track is in the  
> >> Mapping and Sequencing Tracks section, but the data is not  
> >> available on the Table Browser (presumably because of the changing  
> >> nature of the track, depending on user input). Is there a way to  
> >> make the feature both user-changeable AND Table-Browsable? (might  
> >> this involve making the Short Match feature part of the Custom  
> >> Track field?)
> >>
> >> Thank you very much,
> >> Tim
> >>
> >>
> >> Timothy Hefferon, PhD
> >> Research Fellow
> >> Genome Technology Branch
> >> National Human Genome Research Institute
> >> National Institutes of Health
> >> 50 South Dr., Rm. 5525
> >> Bethesda, MD 20892-8004
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>