[Bioperl-l] Intron and exon information

[David Block]

This is kind of in my area - although I've been stuck in Java-land for a while.

These 'files' of yours - what format are they in - just FASTA?

The alignments are done, right?  So what you need to do is figure out where the introns are, and then deduce the phase?

You're going to have to create a Bio::SeqFeature::GeneStructure::Gene object, and use its intron capabilities.  Take a look at the perldoc for that module, see if you can shoehorn your data into there, and then I think Hilmar's excellent work will give you the intron data.

Let us know if this helps.

--
David Block                    dblock@gnf.org
GNF - San Diego, CA        http://www.gnf.org     
Genome Informatics  /  Enterprise Programming

> -----Original Message-----
> From: Lars G. T. Jorgensen [mailto:larsj@diku.dk]
> Sent: Friday, June 14, 2002 6:50 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Intron and exon information
> 
> 
> 
> 
> I am about to start on a program that can do the following:
> Take a number of files with Genomic DNA and some aligned protein
> sequences and from these inputs generate and output showing the
> protein sequences with the phase of the introns. 
> 
> I have been looking at the sequence I/O classes and the sequence
> classes but my first impression is that there is no way of getting
> information about introns out of a sequence. Is this a correct
> observation?
> 
> -- 
> Mvh|Regards, Lars
> System administrator     | Student 
> Bioinformatics Centre    | Department of Computer Science  
> University of Copenhagen | University of Copenhagen
> http://www.binf.ku.dk    | http://www.diku.dk
> When's the last time you used duct tape on a duct? -- Larry Wall
> 
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