Title :

Faster exact distributions of pattern statistics through sequential elimination of states

Author(s) :

Martin, Donald [Auteur]
Noé, Laurent [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]

Journal title :

Annals of the Institute of Statistical Mathematics

Pages :

231--248

Publisher :

Springer Verlag

Publication date :

2017-02

ISSN :

0020-3157

HAL domain(s) :

Informatique [cs]
Sciences du Vivant [q-bio]
Mathématiques [math]/Probabilités [math.PR]
Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

When using an auxiliary Markov chain (AMC) to compute sampling distributions, the computational complexity is directly related to the number of Markov chain states. For certain complex pattern statistics, minimal deterministic ...
Show more >When using an auxiliary Markov chain (AMC) to compute sampling distributions, the computational complexity is directly related to the number of Markov chain states. For certain complex pattern statistics, minimal deterministic finite automata (DFA) have been used to facilitate efficient computation by reducing the number of AMC states. For example, when statistics of overlapping pattern occurrences are counted differently than non-overlapping occurrences, a DFA consisting of prefixes of patterns extended to overlapping occurrences has been generated and then minimized to form an AMC. However, there are situations where forming such a DFA is computationally expensive, e.g., with computing the distribution of spaced seed coverage. In dealing with this problem, we develop a method to obtain a small set of states during the state generation process without forming a DFA, and show that a huge reduction in the size of the AMC can be attained.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL