From regular expressions to deterministic automata
Theoretical Computer Science
The distribution of subword counts is usually normal
European Journal of Combinatorics
Automata and formal languages: an introduction
Automata and formal languages: an introduction
A unified approach to word statistics
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
A unified approach to word occurrence probabilities
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Average Case Analysis of Algorithms on Sequences
Average Case Analysis of Algorithms on Sequences
Automata and Computability
Theoretical Computer Science
A Statistical Method for Finding Transcription Factor Binding Sites
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
| Hi-index | 0.00 |
In previous work [10], we considered algorithms related to the statistics of matches with words and regular expressions in texts generated by Bernoulli or Markov sources. In this work these algorithms are extended for two purposes: to determine the statistics of simultaneous counting of different motifs, and to compute the waiting time for the first match with a motif in a model which may be constrained. This extension also handles matches with errors. The package is fully implemented and gives access to high and low level commands. We also consider an example corresponding to a practical biological problem: getting the statistics for the number of matches of words of size 8 in a genome (a Markovian sequence), knowing that an (overrepresented DNA protecting) pattern named Chi occurs a given number of times.