[Bioperl-l] FW: Hash table creator

[Heikki Lehvaslaiho]

Sorry. 8-)

I tested your script. It works, but loading is really slow.  ~1.0 sec
on a reasonable SIG workstation and ~3 sec in my laptop (printing
disabled). CodonTable loads in <.022 sec. We better leave it as it is
now; especially when ambiguity does not slow it down that much any
more.

Keep suggesting improvements,

	-Heikki

"Karger, Amir" wrote:
> 
> OK, Heikki. This may be useless, now that you've rewritten CodonTable, but
> since I wasted so much time yesterday, I'll send it along anyway.
> 
> I decided to create
> a program that creates a hash table to translate ANY three letter
> codon into the correct amino acid, including codons with ambiguous
> letters, as well as the ambiguous amino acid outputs.
> 
> The idea would be to put this into CodonTable->new() (with maybe some
> caching
> so that you only call it if you haven't yet called it for a
> codon table with this ID number yet).
> 
> If you run the attached code, you *should* get a list of
> amino acids, and the codons that can possibly create them.
> (Note that the ambiguous amino acids can only be created by
> ambiguous codons.)
> 
> Surprisingly, even though it has to go through 4900 or so combinations,
> it only takes a second or so to run.
> 
> Amir Karger
> CuraGen Corporation
> 
>   ----------------------------------------------------------------------
>                                Name: amino_ambiguous.pl.gz
>    amino_ambiguous.pl.gz       Type: GNU compressed data (appication/x-GNU-compressed)
>                            Encoding: base64
>                         Description: amino_ambig

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