Prediction of complete gene structures in human genomic DNA.

@article{Burge1997PredictionOC,
  title={Prediction of complete gene structures in human genomic DNA.},
  author={Christopher B. Burge and Samuel Karlin},
  journal={Journal of molecular biology},
  year={1997},
  volume={268 1},
  pages={
          78-94
        }
}
We introduce a general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions. Distinct sets of model parameters are derived to account for the many substantial differences in gene density and structure observed in distinct C + G compositional regions of the human genome. In addition… 
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References

SHOWING 1-10 OF 88 REFERENCES

Identification of protein coding regions in genomic DNA.

A computer program, GeneParser, which identifies and determines the fine structure of protein genes in genomic DNA sequences and can rapidly generate ranked suboptimal solutions, each of which is the optimum solution containing a given intron-exon junction is developed.

Prediction of gene structure.

Evaluation of gene structure prediction programs.

The results indicated that the predictive accuracy of the programs analyzed was lower than originally found, which indicates that the programs are overly dependent on the particularities of the examples they learn from.

Gene recognition via spliced sequence alignment.

A spliced alignment algorithm and software tool that explores all possible exon assemblies in polynomial time and finds the multiexon structure with the best fit to a related protein.

A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA

A Generalized Hidden Markov Model (GHMM) provides the framework for describing the grammar of a legal parse of a DNA sequence and provides simple solutions for integrating cardinality constraints, reading frame constraints, "indels", and homology searching.

Predicting Pol II promoter sequences using transcription factor binding sites.

A computer program, PROMOTER SCAN, has been developed to recognize a high percentage of Pol II promoter sequences while allowing only a small rate of false positives, and is now being developed for public distribution.

Large exon size does not limit splicing in vivo

It is concluded that a limitation in exon size is not part of the exon definition mechanism, and plasmid clones containing exon inserts of defined sizes are tested.

Selection of splice sites in pre-mRNAs with short internal exons

Model pre-mRNAs containing two introns and three exons, derived from the human beta-globin gene, were used to study the effects of internal exon length on splice site selection, suggesting that a balance between the length of the uninterrupted polypyrimidine tract and thelength of the exon is an important determinant of the relative strength of the splice sites, ensuring correct splicing patterns of multiintron pre- mRNAs.

GENMARK: Parallel Gene Recognition for Both DNA Strands

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

The precision of this approach is better than other methods and has been tested on a larger data set, and a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.
...