Generating Random Genomic Sequences and Structures with GenRGenS

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Generating Random Genomic Sequences and
Structures with GenRGenS
Yann Ponty Michel Termier Alain Denise
Laboratoire de Recherche en Informatique - UMR
8623 - Orsay Institut de Génétique et
Microbiologie - UMR 8621 - Orsay
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random sequences
random sequences
random sequences
random sequences
random sequences
random sequences
random structures
random sequences
random sequences
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Random sequences/structures Why ?

• Significance ( P-value, Z-score )
• Sensibility of algorithms
• Thresholds for bioinformatic methods
• Algorithmic complexity
• Properties of null-models
• Experimental validation of models

Probability for an observed phenomenon to happen
under a given null hypothesis ?
Probability for a heuristic detection algorithm
to find its target ?
Above which score do we investigate a finding ?
What is the average relationship between the size
of the input (sequence length, number of bases)
and the time consumed by a program ?
What remains to be explained and added to the
model ?
Perfect validation of a model Generate from
model and test in vivo !
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Models for random sequences

• Sequences
• Standard/Framed Markov/HMMs
• PROSITE Patterns
• Structures
• Regular Expressions
• Weighted Context Free Grammars
• Hierarchical Models

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Models for random sequences

• Sequences
• Standard/Framed Markov HMMs
• PROSITE Patterns
• Structures
• Regular Expressions
• Weighted Context Free Grammars
• Hierarchical Models

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Want to know more about random generation and the
way GenRGenS performs its task ?
Meet us at poster 68 !!!
Or visit GenRGenS homepage
http//www.lri.fr/genrgens
Thank you for your attention !