[BioC] extract introns

[Ivan Gregoretti]

Hello Yating,

For example, this is how you get a sequence of 50 nucleotides from
murine chromosome 1:

library(Biostrings)

library(BSgenome.Mmusculus.UCSC.mm9)

Views(Mmusculus[["chr1"]],IRanges(start=3000001,end=3000050))

 Views on a 197195432-letter DNAString subject
subject: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...AAAGAATTTGGTATTAAACTTAAAACTGGAATTC
views:
     start     end width
[1] 3000001 3000050    50 [GAATTCTTTTCTATGATTTAGTTTAATATGTTTTCTGGGTGTTTCAGCTG]
Warning message:
In Views(Mmusculus[["chr1"]], IRanges(start = 3000001, end = 3000050)) :
 masks were dropped


One more thing. Next time, before you ask a question about a package,
please make sure you have read the package documentation entirely. I
am responding to you this time because I once asked this same question
before reading all the documentation!

Ivan




On Wed, Nov 9, 2011 at 6:22 AM, Yating Cheng <yating.cheng at charite.de> wrote:
> Dear Bioconductor Memebers,
>
> Now I have to extract intron sequences, I have already exon+intron, intron
> sequences. Someone told me that I can use Biostring. But I tried, it
> failed.
>
> Do you know how to use Biostring to solve this problem, or is there any
> other possibility to solve this problem?
>
> Thanks very much.
>
> Best Regards
>
> Yating Cheng
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>