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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
Comments: To: peter.crawford@db.com
Content-Type: text/plain; charset=us-ascii

This is my reply to Peter Crawford that I am sharing with the list.

--- peter.crawford@db.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 > starts > a macro variable holding the first accepted > sequence

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.

steve

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