Prediction of MARs/SARs in genomic sequences ?
dellaire at odyssee.net
Tue Jan 21 13:46:07 EST 1997
From: John Greally <greally at BIOMED.MED.YALE.EDU
To: genstruc at net.bio.net
Subject: Re: Prediction of MARs/SARs in genomic sequences ?
Date: Tuesday, January 21, 1997 12:57 PM
>Does anyone know if MARs/SARs can be predicted solely from the
>primary sequence ? If yes, is there any computer program to
>detect potential MARs in genomic sequences (human, drosophila,
>nematode, yeast, etc.) ?
>Thank you for your help,
You should look at the article by Kramer and Krawetz in Genomics (1996
33 305-308). There are some problems with their analysis, but it's a
good starting point.
As regards whether they can be predicted solely from DNA sequence, the
answer is no. I find that sequence with few MAR motifs is always
negative in nuclear matrix binding assays, while sequence with many
motifs is often but not always positive. Where 'few' ends and 'enough'
motif density begins is also completely unknown. The nuclear matrix
binding assay remains the gold standard.
John M. Greally 203.785 4353 lab
Department of Genetics, I 134 203.785 7023 fax
Yale University School of Medicine 860.340 3965 beeper
333 Cedar Street, P.O. Box 208005
New Haven, CT 06520-8005, USA. greally at biomed.med.yale.edu
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