[BioRuby] transcription factor binding site identification

[Toshiaki Katayama]

Hi,

If you want to search with TRANSFAC motifs, you can use the tfscan command in the EMBOSS package.

Otherwise, you may need to define your own algorithm to search your motif.
If your motif is in profile format, you need to develop profile search method.
If your motif is simple and can be converted to regexp, the task would be relatively easy.

  # to find all occurrences
  results = seq.scan(regexp)

  # to find positions of match
  pos = 0
  while pos = seq.index(regexp, pos + 1)
    puts pos
  end

You may also interested in the Bio::Sequence#window_search method.

Thanks,
Toshiaki

On 2007/11/05, at 5:32, Bernd Jagla wrote:

> Hi there, 
>
>
>
> Is it possible with bioruby/ruby to scan a nucleotide sequence and search
> for binding sites of TFs?
>
>
>
> How would I do this? (I looked in the documentation but couldn't find it.)
>
>
>
> Thanks,
>
>
>
> Bernd
>
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