## Automatic Translation PATCH ##

risler at cgmvax.cgm.cnrs-gif.fr risler at cgmvax.cgm.cnrs-gif.fr
Tue Feb 21 12:48:02 EST 1995

> Regarding the automatic translation question that was posed earlier ...
> Yes it does exist in Version8 of GCG but only at the commandline.  The
> command is:
> 	PepData
> It translates your nucleotide sequence into all six reading frames 
> forward and three backwards) then concatenates them for you.

I'm afraid this definitely does NOT answer the question.

Suppose I want to extract (and possibly translate on the fly) the sequence 
of human lysozyme. Its DNA sequence contains several introns and exons. To 
date, the only way with GCG (as far as I know) is to display the Genbank 
(or EMBL) sequence, take a sheet of paper and a pencil, note the 
boundaries of each exon, quit the editor or whatever was used to display 
the sequence, run ASSEMBLE and feed it manually with all the boundaries. 
It's a pain in the neck and error prone process !!

That's precisely why the JOIN feature was included in the databanks. For 
intervening sequences, it makes a summary of the boudaries of individual 
exons (example JOIN   234..522  744..1240  1724..2167). You may even find 
exons in another entry (because many sequences are not concatenated) such 
as JOIN 537.. 832 X12678:1290..1856

Obviously, this can be handled easily by a computer. And it IS, in fact, 
handled by SRS or ACNUC. With these programs, you just have to type the 
name of the splitted gene you want to extract (and possibly translate on 
the fly), and here you are (provided, of course, that the JOIN feature 
exists in the entry).

Suppose you want to extract a splitted gene called SCHMURTZ from yeast 
chromosome III. Will you really run pepdata and translate the 350,000 bp 
sequence in all six reading frames? 

Thus I stick to my previous opinion: the fact that TRANSLATE or ASSEMBLE 
in GCG are not able to use the JOIN feature is a major miss.


Jean-Loup       risler at cgmvax.cgm.cnrs-gif.fr

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