[BioC] assemble DNAString complete coding sequence from exons?

Hervé Pagès hpages at fhcrc.org
Tue Mar 24 23:34:41 CET 2009

Hi Paul,

Yes, we need a better (and more efficient) way.
This, as well as support for subsequence replacement (via subseq<-) that
you just asked me off-list, is on its way. Should be ready later today or
tomorrow. Thanks for your patience.


Paul Shannon wrote:
> I am sure there is an elegant way to do this.  Could somebody clue me in?
> I have (in a simple case) two exons for a gene on the + strand, and a 
> the full DNAString sequence of its chromosome.
> My naive technique for constructing a DNAString of the entire coding 
> sequence is
>   1) paste together toString (subseq (seq.chrom, exon.start, exon.end)) 
> for each exon
>   2) construct a DNAString from the resulting chars.
> There must be a better way.  What is it?
> Thanks!
>  - Paul
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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