Performance Evaluation of DNA MOTIF discovery programs
نویسندگان
چکیده
منابع مشابه
Performance evaluation of DNA Motif discovery programs
Methods for the identification of transcription factor binding sites have proved to be useful for deciphering genetic regulatory networks. The strengths and weaknesses for a number of available web tools are not fully understood. Here, we designed a comprehensive set of performance measures and benchmarked sequence-based motif discovery tools using large scale datasets (derived from Escherichia...
متن کاملRetraction for Singh et al. Performance evaluation of DNA Motif discovery programs
[This retracts the article on p. 205 in vol. 3, PMID: 19255635.].
متن کاملMotif discovery programs
BayesMD [1] is a probabilistic, Bayesian model for predicting novel transcription factor binding sites. Biological information about binding sites properties, background sequence models, occurrence and positional preferences are built into the model in modular fashion. Mixture prior parameters for the motif and background are trained using information on TFBSs and organismspecific promoter sequ...
متن کاملAutomated DNA Motif Discovery
Ensembl’s human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene.
متن کاملDevelopment of an Efficient Hybrid Method for Motif Discovery in DNA Sequences
This work presents a hybrid method for motif discovery in DNA sequences. The proposed method called SPSO-Lk, borrows the concept of Chebyshev polynomials and uses the stochastic local search to improve the performance of the basic PSO algorithm as a motif finder. The Chebyshev polynomial concept encourages us to use a linear combination of previously discovered velocities beyond that proposed b...
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ژورنال
عنوان ژورنال: Bioinformation
سال: 2008
ISSN: 0973-8894,0973-2063
DOI: 10.6026/97320630003205