[Biojava-l] Sequence start/end location

Mark Schreiber markjschreiber at gmail.com
Sat Jan 31 04:15:59 UTC 2009

Hi -

Unfortunately your FASTA file won't contain any feature information
which could tell you the start and end. If you don't want to get the
info from the PTT file you might want to look at parsing the Genbank
file instead which will have the feature information.

A PTT parser might not be a bad thing for BioJava though. If you write
one please consider adding it.

- Mark

On Sat, Jan 31, 2009 at 10:41 AM, Hamed, Ahmed A.
<ahmed.elmasri at gmail.com> wrote:
> Hello list,
> I am trying to get find the start and end location of a gene in a gene
> sequence. I am reading from a gene FASTA database file. Is there a built-in
> method that I can use? The alternative is really painful since I have to
> parse a ptt file and not exactly working for me.
> Thanks very much!
> Ahmed
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