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Handling EST sequences

Jeremy.Parsons jeremy.parsons at mciworld.com
Sat Jul 10 20:37:58 EST 1999

I think Phil Green prefers to use unclipped reads in assemblies so you might
want to check phred's trim_alt function very carefully on your own data
before committing yourself to that route for sequencing vector clipping.
The Staden package seems more flexible to me. If your assemblies
really are simple (only joining forward and reverse) I think you will
find anything will work well. On the other hand, you are wise to ask
on bionet if your problem turns out to be more complex. If you are
interested in EST clustering you have more options again. Phrap is
great for complex genomic assemblies but I'm not fond of all the new
file formats (.phd .qual etc) and you might find the old Staden Experiment
files whilst complicated actually records information you may later need.


Felipe Rodrigues da Silva wrote:

> We are just starting an EST project (sugar-cane). Despite the fact that
> I do think Staden is far much more complete than phred/phrap/consed (and
> I have a personal bias in loving the former), the solution found to
> manage data here was to use the latter (phred/phrap) to analyze and
> generate the fasta files we need. All requirements proposed in your
> message are done by scripts that call components of phred/phrap.
>      I would be very interested in hearing from anyone using Staden in
> EST projects.
>                 Felipe.
> "l. heijnen" wrote:
> >
> > Hi,
> >
> > We are currently evaluating software packages that are able to analyse short
> > (<500 bp)EST sequences in a high-trougput, automated mode.
> >
> > We are determining the EST sequences on an ABI 377.
> > We would like to have base calls with quality scores.
> > Vector sequences should be trimmed off automatically.
> > Some (basic) assembly should be possible (forward/reverse run).
> > Editting should be possible on trace files.
> > Output sequences should be in Fasta format.
> > The complete process should be fast (with very little "hands on work")
> >
> > Would the Staden package be a good choice to handle this job?
> > Are there any other suggestions?
> >
> > Thanks
> >
> > L.heijnen at hccnet.nl
> --
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