<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Hilton. Thanks for your suggestion. <br></span></div><div><br></div><div><br><span></span></div><div><span>I saw re module. I should have explain a little bit in my message that patter of polymer is not constant. There could be variety of combinations given A, T G and C. <br></span></div><div><span></span><span>it could be AAATAAA, ATATATAT, or GTAGTAGTA or GGGACCCGAAAT etc.<br></span></div><div><span></span><br></div><div>so I do not know what that pattern would be when I read in a string. I do not know if regex could solve my kind of problem too. <br></div><div><br></div><div>Thanks</div><div>Hs.<br></div><div><br><span></span></div><div><br></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif;
font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Hilton Fernandes <hgfernan@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> "tutor@python.org" <tutor@python.org> <br><b><span style="font-weight: bold;">Cc:</span></b> Hs Hs <ilhs_hs@yahoo.com> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, January 19, 2012 1:39 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [Tutor] finding a polymer of letters in a string<br> </font> </div> <br>
<div id="yiv1262557614">Hi ! <div><br></div><div>Have you considered regular expressions in Python ? </div><div><br></div><div>Please take a look at "Regular Expression HOWTO", at </div><div>http://docs.python.org/howto/regex.html</div>
<div><br></div><div>All the best, </div><div>Hilton <br><br><div class="yiv1262557614gmail_quote">On Thu, Jan 19, 2012 at 4:09 PM, Hs Hs <span dir="ltr"><<a rel="nofollow" ymailto="mailto:ilhs_hs@yahoo.com" target="_blank" href="mailto:ilhs_hs@yahoo.com">ilhs_hs@yahoo.com</a>></span> wrote:<br>
<blockquote class="yiv1262557614gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="font-size:12pt;font-family:times new roman, new york, times, serif;"><div>Hi: </div><div>I am writing to see if I could any help.</div>
<div>I am trying to find if a mutation in gene falls in a polymer region of DNA. To explain in simplistic terms, <br></div><div><br></div><div>Given a piece of DNA string, with following characters, I know where mutation happens. Happens at T (in quotes with spaces.) 3 As before T and 4 As after T are removed in a disease. <br>
</div><div><br></div><div>Given following sequence, I should be able to find if this T is in a polymer region. such as 'AAA' T 'AAAA. <br></div><div><br></div><div>AAATAGCAGAAA 'T' AAAAGAAAAGATTGGAACTAGGTCAG</div>
<div><br></div><div><br></div><div><br></div><div>I am not sure if there are any methods in python to find these. Do you think a script has to be written with more logic involving some known algorithms.
<br></div><div><br></div><div>Please advise. <br></div><div><br></div><div>thanks</div><span class="yiv1262557614HOEnZb"><font color="#888888"><div>Hs.<br></div></font></span></div></div><br>_______________________________________________<br>
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