[Bioperl-l] longest ORF

Dan Kortschak Dan Kortschak <kortschak@rsbs.anu.edu.au>
Thu, 1 Aug 2002 11:30:11 +1000 (EST)


  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

--98048-366868266-1028165411=:23010
Content-Type: TEXT/PLAIN; charset=US-ASCII

Done, and with docs. Any errors (biological): please feel free to correct
them.

Dan

On Wed, 31 Jul 2002, Brian Osborne wrote:

> Dan,
>
> >> (if its worth putting in as a demo
> >> script or including - after OOing and making it accept strict it a bit -
> >> please let me know):
>
> Yes, it's a neat example script and one that's oft-requested. Make it strict
> and I or we will put it into the examples/ directory under your name.
>
> Brian O.

-- 
_____________________________________________________________   .`.`o
                                                         o| ,\__ `./`r
  Dan Kortschak    kortschak@rsbs.anu.spanner.edu.au     <\/    \_O> O
                                                          "|`...'.\
  Before you criticise a man, try to walk a mile in his    `      :\
  shoes. Then, if he doesn't like what you have to say,           : \
  you'll be a mile away, and you'll have his shoes.               :  \

  The address above will not work, remove the spanner from the works.

By replying to this email you implicitly accept that your response may
be forwarded to other recipients.
Permission is granted for fair use reproduction.

--98048-366868266-1028165411=:23010
Content-Type: TEXT/PLAIN; charset=US-ASCII; name=longorf
Content-Transfer-Encoding: BASE64
Content-ID: <Pine.LNX.4.44.0208011130110.23010@sunya.rsbs.anu.edu.au>
Content-Description: 
Content-Disposition: attachment; filename=longorf
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--98048-366868266-1028165411=:23010--