[BioC] ProbeID: how to find which one is close to 3 prime end of DNA- help,

[Steve Lianoglou]

> so, I got coordinates of probe sequence alignments then if strand is (+) then take largest "start" number and if strand is (-) then take smallest start number which gives me closest position of probes on 3 prime end.

I'm not sure if you are asking a question, but I can't really make
exact sense of what you're saying, since I'm left to guess at a few
things?

It sounds like you already have probeid <-> gene mappings?
And now you want to go gene-by-gene and look at where each probe for
that genes aligns to the genome?
Then you want to find the 3'-most probe in each such group?

You mention "if strand is (+)". Are you talking about the strand the
probe aligns to (then what you say is wrnog)? Or the strand of the
gene you are currently looking  at (then what you say is maybe right)?

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact