Poisson process approximation for sequence repeats, and sequencing by hybridization.
J Comput Biol
; 3(3): 425-63, 1996.
Article
em En
| MEDLINE
| ID: mdl-8891959
ABSTRACT
Sequencing by hybridization is a tool to determine a DNA sequence from the unordered list of all l-tuples contained in this sequence; typical numbers for l are l = 8, 10, 12. For theoretical purposes we assume that the multiset of all l-tuples is known. This multiset determines the DNA sequence uniquely if none of the so-called Ukkonen transformations are possible. These transformations require repeats of (l-1)-tuples in the sequence, with these repeats occurring in certain spatial patterns. We model DNA as an i.i.d. sequence. We first prove Poisson process approximations for the process of indicators of all leftmost long repeats allowing self-overlap and for the process of indicators of all left-most long repeats without self-overlap. Using the Chen-Stein method, we get bounds on the error of these approximations. As a corollary, we approximate the distribution of longest repeats. In the second step we analyze the spatial patterns of the repeats. Finally we combine these two steps to prove an approximation for the probability that a random sequence is uniquely recoverable from its list of l-tuples. For all our results we give some numerical examples including error bounds.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Distribuição de Poisson
/
Análise de Sequência de DNA
/
Hibridização de Ácido Nucleico
Limite:
Humans
Idioma:
En
Revista:
J Comput Biol
Assunto da revista:
BIOLOGIA MOLECULAR
/
INFORMATICA MEDICA
Ano de publicação:
1996
Tipo de documento:
Article
País de afiliação:
Estados Unidos