Bayesian approach to DNA segmentation into regions with different average nucleotide composition

Vsevolod Makeev, Vasily Ramensky, Mikhail Gelfand, Mikhail Roytberg, Vladimir Tumanyan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Citations (Scopus)

Abstract

We present a new method of segmentation of nucleotide sequences into regions with different average composition. The sequence is modelled as a series of segments; within each segment the sequence is considered as a random sequence of independent and identically distributed variables. The partition algorithm includes two stages. In the first stage the optimal partition is found, which maximises the overall product of marginal likelihoods calculated for each segment. To prevent segmentation into short segments, the border insertion penalty may be introduced. In the next stage segments with close compositions are merged. Filtration is performed with the help of partition function calculated for all possible subsets of boundaries that belong to the optimal partition. The long sequences can be segmented by dividing sequences and segmenting those parts separately. The contextual effects of repeats, genes and other genomic elements are readily visualised.

Original languageEnglish
Title of host publicationComputational Biology - 1st International Conference on Biology, Informatics, and Mathematics, JOBIM 2000, Selected Papers
EditorsOlivier Gascuel, Marie-France Sagot
PublisherSpringer Verlag
Pages57-73
Number of pages17
ISBN (Print)3540422420, 9783540422426
DOIs
Publication statusPublished - 2001
Externally publishedYes
Event1st International Conference on Biology, Informatics and Mathematics, JOBIM 2000 - Montpellier, France
Duration: 3 May 20005 May 2000

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2066
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference1st International Conference on Biology, Informatics and Mathematics, JOBIM 2000
Country/TerritoryFrance
CityMontpellier
Period3/05/005/05/00

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