Bioperl: Q: extracting upstream regions

[Ewan Birney]

On Wed, 31 Mar 1999, gert thijs wrote:

> Hello,
> 
> I have 2 questions:
> - Is there a FAQ or manual available on the bioperl distribution?

Have you looked at the web site http://bio.perl.org? To see the FAQ,
go to FAQ - (it is a little light- if your question is not answered,
please let us know, and we will answer it).

Documentation can be found off the 'download' section. Start with
bioperl.pod which gives you an overview.

If/when you donwload the distribution, look in the example directory
to get an idea about how to use the modules.


> - I've written some perl-scripts to split dna sequences in windows and to
> search for consensus sequences. but now I like to extract the upstream region
> of a gene form a sequence. In my current script I have to fill in the postion
> of the start codon of each gene in the sequence and I us this position to
> extract the region of interest. But this is a very complicated way of working,
> especially if I would like to work with larger data sets. As I'm not used to
> the bioperl distribution, I cannot find the if there are usefull procedures in
> bioperl. Can someone give some hints? (if there's a positive answer to the
> first question I probably will find the answer two the second question myself
> :-)
> 

To be honest, I don't think you will have much luck in bioperl, though
the ability for the sequence object to truncate from xxx to yyy might be
useful.

Where are you getting the information about the start point? (from the
embl feature table?).

Good luck. If you want any more help, do just email again.

> Gert Thijs
> 
> -- 
> ==========================================================
> + Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
> +                                                        +
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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