Emig, Robin wrote:
> 4) What about the idea of just creating a new object called CodonBiasTable,
> which has all of these ideas added, plus the frequency weights? It could be
> based off of an internal translation table, and distribution.
> -Robin
You will get the most mileage out of the CodonBi
Sounds good, but I do like the idea of including start/stop codons in the
class.
Robin
-Original Message-
From: Matthew Pocock [mailto:[EMAIL PROTECTED]]
Sent: Wednesday, August 29, 2001 3:09 AM
To: Emig, Robin
Cc: 'Keith James'; BioJava List
Subject: Re: [Biojava-l] Translation tables an
Emig, Robin wrote:
> Sounds good, but I do like the idea of including start/stop codons in the
> class.
> Robin
By all means. How about a:
// returns a Symbol with a getMatches() that will match
// exclusively to start codons
Symbol getStartCodons();
Does that look OK?
Matthew
>
>
looks good, with one for stop as well
-Robin
-Original Message-
From: Matthew Pocock [mailto:[EMAIL PROTECTED]]
Sent: Wednesday, August 29, 2001 9:41 AM
To: Emig, Robin
Cc: 'Keith James'; BioJava List
Subject: Re: [Biojava-l] Translation tables and Met
Emig, Robin wrote:
> Sounds good,
I've just commited new code to map AceDB sequence objects into BioJava
sequences. It is very ropey code, and I have only checked that it
compiles, not even that it works for a test case. It is checked into
org.acedb.seq package in biojava-acedb. If anybody is keen, it would be
fun to hack the
A codon bias table would also be good for making gene finding HMM's esp if
it included dicodon pairs, hint hint ;-)
Mark
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
> -Original Message-
> From: Emig, Robin [mailto:[EMAIL PRO
