Date: Wed, 17 Nov 1999 10:05:29 -0800
Reply-To: Stephen Arthur <sarthur67@YAHOO.COM>
Sender: "SAS(r) Discussion" <SAS-L@LISTSERV.UGA.EDU>
From: Stephen Arthur <sarthur67@YAHOO.COM>
Subject: Re: Stepping through a sequence of data until a criteria is met
Content-Type: text/plain; charset=us-ascii
This is my reply to Peter Crawford that I am sharing
with the list.
--- email@example.com wrote:
> There are some really effective and simple things
> that you can do with character
> variables and functions, but...
That is what I was thinking (maybe deleting the first
observation after a test fails, and then continue with
the step from there), but...
> How do your items arise?
> separate variables 1 char long
> one long string
> separate observations
> external text file
> macro variable
The data is imported from a gene sequence file a
scientist with a 'SEQ File' format.
This data was orginal one long sequence of 1276
characters (ATCG). The scientist is interested in
certain segments along this sequence.
I separated the sequence using the replace function in
word to replace 'A' w/ ' A ' (I am doing this on the
fly) to create separate observations.
> What would the likely maximum be for that arbitrary
> 73 ?
> no more than 200
> frequently over 200, but under 32768
This will be the case:
"frequently over 200, but under 32768"
> What output do you want from the algorithm ?
> one observation for each set of 50 bases
> one observation per accepted sequence
> the first accepted sequence
> the position where the first accepted sequence
> a macro variable holding the first accepted
The output I would like is a sequence of 50 bases from
a segment containing 50% or more CG content.
From there I need to find a 45 base segment that is
contained in the 50 base segment, all the way down to
a 10 base segment from the previous 5 base step w/ at
least 50% CG content.
> Fascinating question -- what is the application
> generating this requirement ?
The 50% CG rule requirement meets a criteria for
picking a possible probe the scientists can use to
direct their experiments.
Thanks for your help.
I need to think this through more.
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