[BioC] intragenic sequence extraction

[Yating Cheng]

Hi Steve

Thank you for your answer. Then I ran this script, but there is error in
the end. And I don't know how to solve it.

library(Biostrings)
library(GenomicRanges)


library(BSgenome.Amellifera.UCSC.apiMel2)
bee.txdb<- makeTranscriptDbFromUCSC(genome="apiMel2",
  tablename="ensGene")
  tx <- transcripts(bee.txdb, columns=c("tx_id", "tx_name", "gene_id"))


intragenic_seq<-getSeq(Amellifera,gaps(tx))

#####Error in .starfreeStrand(strand(names)) :
  cannot mix "*" with other strand values



Yating





> Hi,
>
> On Tue, Nov 29, 2011 at 6:25 AM, Yating Cheng <yating.cheng at charite.de>
> wrote:
>> Dear All,
>>
>> Does anyone know that how to extract intragenic sequences from the
>> genome.
>>
>> Like in the genescan, it is mentioned that the predictions are based on
>> transcriptional, translational and donor/acceptor splicing signals as
>> well
>> as the length and compositional distributions of exons, introns and
>> intergenic regions.
>>
>> But I am not sure which function I should use.
>
> Use the GenomicFeatures package to build a gene annotation database
> for your organism. By getting a bit more intimate with that package
> (good place to start is by reading its vignette, along with that for
> GenomicRanges) you will figure out how to identify where the
> intergenic regions lie on your genome.
>
> Once you have the intergenic regions of your genome stored in a
> GRanges object, its easy to use those ranges to get the sequence from
> your genome using the appropriate BSgenome.* package for your
> organism. The Biostrings::getSeq function could do that for you, among
> other things.
>
> HTH,
> -steve
>>
>>
>> Thank you very much.
>>
>>
>>
>>
>> Yating Cheng
>> Molecular Medicine Master's Program
>> Charité-Universitätsmedizin Berlin
>>
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>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>