Automatic translation

Per Villand pevillan at bioslave.uio.no
Fri Feb 17 07:59:20 EST 1995

In article <1995Feb17.103328.1596 at comp.bioz.unibas.ch> doelz at comp.bioz.
unibas.ch (Reinhard Doelz) writes:

>: Why is there in GCG no program (or is there?) that translates an EMBL/
>: Genbank DNA sequence file automatically to an amino acid sequence file 
>: according to the information for transcription, splicing and translation 
>: provided in the file? It is quite boring to do this manually, and should be 
>: an easy task for a computer.
>The SRS program from Thure Etzold can do this, either based on local data
>bases, or via network using the SRSWWW browser. Check out the SRS servers 
>at http://www.embl-heidelberg.de/srs/status.html or, alternatively, on 
>http://www.ch.embnet.org/srs/status.html . Thure  and his team have also 
>written a program called 'TREMBL' which will translate an entire database. 

I still think it would be very useful with a program in GCG (or just on the 
machine where the sequence analysis is done) that could do automatic 
translation. For instance: I do a FASTA or TFASTA search, and get a list of 
10 files in the database with homology to my sequence. I then want to have 
an multi-alignment of the amino acid sequences for the 11 genes. The way I 
do it now, is that I FETCH each of the sequences, look in the sequence 
information for each of them for how they are translated and write down on 
paper, ASSEMBLE an intron-free sequence based on that information, TRANSLATE 
to get the amino acid sequence, and lastly do PILEUP. This takes a lot of 
time, and would be much easier and faster with automatic translation.

- Per

Per Villand
Plant Molec. Biol. Lab.                                          
Agric. Univ. of Norway
1432 Aas, Norway        
per.villand at embnet.uio.no

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