Complexity reduction in context-dependent DNA substitution models
نویسندگان
چکیده
منابع مشابه
Complexity reduction in context-dependent DNA substitution models
MOTIVATION The modeling of conservation patterns in genomic DNA has become increasingly popular for a number of bioinformatic applications. While several systems developed to date incorporate context-dependence in their substitution models, the impact on computational complexity and generalization ability of the resulting higher order models invites the question of whether simpler approaches to...
متن کاملCoupling times with ambiguities for particle systems and applications to context-dependent DNA substitution models
We define a notion of coupling time with ambiguities for interacting particle systems, and show how this can be used to prove ergodicity and to bound the convergence time to equilibrium and the decay of correlations at equilibrium. A motivation is to provide simple conditions which ensure that perturbed particle systems share some properties of the underlying unperturbed system. We apply these ...
متن کاملAccurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context.
Most models and algorithms developed to perform statistical inference from DNA data make the assumption that substitution processes affecting distinct nucleotide sites are stochastically independent. This assumption ensures both mathematical and computational tractability but is in disagreement with observed data in many situations--one well-known example being CpG dinucleotide hypermutability ...
متن کاملComplexity Reduction of the Context - TreeWeighting
We present a method to decrease the storage and communication complexity of the context-tree weighting method. This method is based on combining the estimated probability of a node in the context tree and weighted probabilities of its children in one single variable. This variable is represented by its logarithm.
متن کاملContext-dependent factored language models
The incorporation of grammatical information into speech recognition systems is often used to increase performance in morphologically rich languages. However, this introduces demands for sufficiently large training corpora and proper methods of using the additional information. In this paper, we present a method for building factored language models that use data obtained by morphosyntactic tag...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2008
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btn598