Analysis of n-Gram based Promoter Recognition Methods and Application to Whole Genome Promoter Prediction
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Summary
A study of n-grams as features for a neural network classifier for E. coli and Drosophila promoters is made and results are encouraging in positive identification of promoters in the genome compared to software packages such as BPROM, NNPP, and SAK.
- Type
- article
- Published
- 2009-02-01
- Cited by
- 20
- References
- 25
- OpenAlex
- https://openalex.org/W1948467576
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:24652915
Keywords
Genome, Promoter, Genetics, Computational biology, Biology
References
- Predicting vertebrate promoters with heterogeneous cluster computing
- Promoter prediction analysis on the whole human genome
- The pitch of chromatin DNA is reflected in its nucleotide sequence.
- POIMs: positional oligomer importance matrices—understanding support vector machine-based signal detectors
- A mammalian promoter model links cis elements to genetic networks.
- Genome-wide analysis of mammalian promoter architecture and evolution
- Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments.
- Computational analysis of core promoters in the Drosophila genome
- A Systematic Computational Approach for Transcription Factor Target Gene Prediction
- The Transcriptional Landscape of the Mammalian Genome
- The Biology of Eukaryotic Promoter Prediction - A Review
- Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.
- Analysis of E.coli promoter recognition problem in dinucleotide feature space
- Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.
- Sequence alignment kernel for recognition of promoter regions
- Prediction of probable genes by Fourier analysis of genomic sequences
- Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
- Identification of transcription factor binding sites with variable-order Bayesian networks
- MetaProm: a neural network based meta-predictor for alternative human promoter prediction
- Eukaryotic promoter recognition.
Cited by
- N-gram analysis of 970 microbial organisms reveals presence of biological language models
- Assessing the Effects of Data Selection and Representation on the Development of Reliable E. coli Sigma 70 Promoter Region Predictors
- Current perspective on bacterial pigments: emerging sustainable compounds with coloring and biological properties for the industry – an incisive evaluation
- Suite of Tools for Statistical n-Gram Language Modeling for Pattern Mining in whole genome Sequences
- Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake
- Recognition of prokaryotic promoters based on a novel variable-window Z-curve method
- Numeric promoter description - A comparative view on concepts and general application.
- Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris.
- bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli
- TSSPlant: a new tool for prediction of plant Pol II promoters
- Advances in Intelligent Systems and Computing
- Benchmarking available bacterial promoter prediction tools: potentialities and limitations
- DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning
- Optimized convolutional neural network–multilayer perceptron for the detection of COVID-alike viruses using genome sequencing data
- Mimicking Transcription Process to Recognise Promoters in E . coli
- Promoter Recognition Using Neural Network Approaches
- Promoter Recognition in human genome Chandrashekar
- In Silico and in Vitro Reverse Genetics of yebV of Escherchia Coli
- A nG-HPR : Analysis of n-Gram based human Promoter Recognition
- Predicting Protein Coding Regions by Six-Base Nucleotide Distribution
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