From: Spouge, John (NIH/NLM/NCBI) [E]
Sent: Monday, April 27, 2009 11:18 AM
To: NLM/NCBI List ncbi-seminar
Subject: NCBI Seminar Apr 28 11:00 am , B2 Floor NCBI Library, Building 38A 

NCBI Seminar Apr 28 11:00 am , B2 Floor NCBI Library, Building 38A 

John Spouge

 

A Rigorous Statistical Theory for Detecting Repeats In Biological Sequences

 

This talk gives a rigorous statistical theory of inexact simple repeats (a.k.a. tandem repeats). A “simple repeat” consists of a particular word of length w repeated several times without gaps; an “inexact simple repeat” permits point mutations to corrupt individual letters in the repeat. Karlin and Dembo extended the statistical theory of local maxima from independent identical summands, as in gapless BLAST, to Markov additive processes. The theory for Markov additive processes provides the statistics of inexact simple repeats. The Ruzzo-Tompa algorithm for maximal segments is a general algorithm for finding local maxima, so its specialization finds gapless inexact repeats in linear time.

 

I will discuss briefly some applications of finding repeats and some future extensions of this work.