>> 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
(three
> 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.
Cheers,
Jean-Loup risler at cgmvax.cgm.cnrs-gif.fr
