From: egrasso.rb@...2.net
Date: 2008-07-15T12:18:09+09:00
Subject: Re: regexp with gaps

Mmmmm... nop. I think I didn't explain the idea very well... I'm writing a
script to find specific secuences of DNA (binding sites) inside of a large
secuence of DNA (for thosse who doesn't know, DNA sequences are made of 4
diferent bases: A, T, C and G). The problem is that the binding sites don't
need to be 100% exact to work. For example, the binding site for an X
protein is "AAATTT", but the protein can also bind to the secuence "AAAGTT"
or "AACGTT" and work fine. I need to find all this sites, but the only data
I have is that "Protein X binds to AAATTT".
I finally solve the problem without using str.index nor regexp, basically,
I seek it manually:

(Note: variables are in spanish!: buscarBS=find binding site,
patron=pattern, semejanza=1 to 0, minimal similarity, cadena=string,
respuesta=answer, largo=length)

def buscarBS(patron, semejanza=0.6, cadena=@secuencia)
  respuesta = ""
  i = 0.0
  j = 0.0
  largoc = cadena.length
  largop = patron.length
  
  while i <= (largoc-largop)
   j = 0.0
   puntos = 0.0
   subpuntos = largop * (1-semejanza)
   
   while (j < largop) and (subpuntos > 0)
    pos = i + j
    if cadena[pos] == patron[j] then
     puntos +=1
    else
     subpuntos -=1
    end 
    j+=1
   end
   if (puntos / largop) >= semejanza then
     respuesta = respuesta + "desde: "+(i+1).to_i.to_s+" hasta:
"+(i+j).to_i.to_s+" - similitud: - "+(puntos / largop * 100).to_s+"%\n"
   end  
   i+=1
  end

  if respuesta == "" then
   respuesta = "No se encontro ninguna secuencia similar (similitud:
#{semejanza} - #{patron})"
  else
   respuesta = "\nSe encontraron las siguientes similitudes:\n\n"+respuesta
  end
  return respuesta

 end

 I still need to polish and optimize the code but it find all possible
sites with at least an specific similarity and tells me how similar they
are. If anyone have another idea, need more details about the code or is
interested in bioinformatic with ruby tell me.
Thanks

On Mon, 14 Jul 2008 23:15:30 +0900, phlip <phlip2005@gmail.com> wrote:
>> The problem is that now I need to
>> find all positions where the pattern matches 12 or more chars.
>> For example: For the pattern "aaaaaa", find substrings "aaaaaa",
>> "aaabaa", "baaaaa", "ababaa", etc
>> 
>> First I thought that I could create all possible patterns (with \w)
> 
>    \w{12,}
> 
> Right?
> 
> Either that or \w{12}\w*