pevillan at bioslave.uio.no (Per Villand) wrote:
>> 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
One way out of these problems is to use programs such as PairWise
or SearchWise which compare a protein sequence or a protein
profile *directly* against a DNA sequence, doing all the translation
etc inside the program.
As a quite big added bonus PairWise and SearchWise allows frameshifting
to occur between the forward and backward frames (you will *not*
believe the number of errors there are in the databases until
you start using this program). In fact with a bit of fiddling with
the parameters you can jump *introns* and still expect to see a
close to optimal alignment.
PairWise can be linked at compile time to GCG8 (you don't need to
recompile GCG). This makes it quite a nice program to use: you
just have it running picking sequences out of GCG8 successively.
(Guess who wrote PairWise and SearchWise?)
And its free....
It could be useful. For more information, you can email me or
the server is distinctly flaky. You can also try
birney at molbiol.ox.ac.ukhttp://www.molbiol.ox.ac.uk/www/users/birney/me.html