[Biojava-l] Translation tables and Met

[Emig, Robin]

1) I would call them by their full name, with possibly and underscore
instead of a space. If that doesn't work (ie for multi organism tables) then
I think we should add a SHORT_NAME, LONG_NAME and DESCRIPTION fields as xml
tags or as parameters. In fact they may be useful anyway.
2) I say we add this to the xml file for translation table. add Extra tags
like <TxInit>ATG</TxInit>. and <TxStop>TAG</TxStop>
3) Alternatively, we could create a separate file with this information as
suggested, but also add other wonderful things that are involved in
Translation (like readthroughs etc)
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

-----Original Message-----
From: Keith James [mailto:kdj@sanger.ac.uk]
Sent: Tuesday, August 28, 2001 3:16 AM
To: BioJava List
Subject: [Biojava-l] Translation tables and Met



Hi all,

Currently we have but one translation table (UNIVERSAL, aka Standard
#1). I would like to add the others:

See http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c

Vertebrate Mitochondrial, #2
Yeast Mitochondrial, #3
Mold, Protozoan, Coelenterate Mitochondrial, Mycoplasma/Spiroplasma, #4
Invertebrate Mitochondrial, #5
Ciliate, Dasycladacean and Hexamita Nuclear, #6

Echinoderm Mitochondrial, #9
Euplotid Nuclear, #10
Bacterial, Plant plastid, #11
Alternative Yeast Nuclear, #12
Ascidian Mitochondrial, #13
Flatworm Mitochondrial, #14
Blepharisma Nuclear, #15
Chlorophycean Mitochondrial, #16

Trematode Mitochondrial, #21
Scenedesmus obliquus Mitochondrial, #22
Thraustochytrium Mitochondrial, #23

This would involve adding to TranslationTables.xml

<table name="VERTEBRATE-M" source="(RNA x RNA x RNA)" target="PROTEIN-TERM">
 <...blah>
</table>

As some of the names are very verbose I'll make a first stab at some
abbreviations to go in the name attribute. I've done a web search for
standard abbreviations and none came up. If any one knows of standard
short names, would they let me know? (It would be nice to refer to them
by their number, but this would mean messing with the XML format.)

 #1 UNIVERSAL (we have this)
 #2 VERTEBRATE-M
 #3 YEAST-M
 #4 MPM-COEL-M
 #5 INVERTABRATE-M
 #6 CD-HEXA-N

 #9 ECHINODERM-M
#10 EUPLOTID-M
#11 BACTERIAL
#12 ALT-YEAST-M
#13 ASCIDIAN-M
#14 FLATWORM-M
#15 BLEPHARISMA-N
#16 CHLOROPHYCEAN-M

#21 TREMATODE-M
#22 SCENEDESMUS-M
#23 THRAUSTOCHYTRIUM-M

All have a second associated table of initiation codons which could
possibly go in a separate file e.g. InitTranslationTables.xml which
would be read at the same time as the main table.

In order to cope with alternative initiation codons we need a new
translate method which can accept two TranslationTables (one for the
initiation codon and one for the other codons) and a new
TranslatedSymbolList which can return Symbols from two different
TranslationTables.

In the case where one is translating a C-terminal part of an mRNA
(i.e. the first codon isn't the initiation codon), one can simply use
the single-table method and get the correct result.

How does this sound?

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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