Computational identification of promoters and first exons in the human genome

Davuluri, R. V., Grosse, I., Zhang, M. Q. (December 2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

URL: http://www.ncbi.nlm.nih.gov/pubmed/11726928
DOI: 10.1038/ng780

Abstract

The identification of promoters and first exons has been one of the most difficult problems in gene-finding. We present a set of discriminant functions that can recognize structural and compositional features such as CpG islands, promoter regions and first splice-donor sites. We explain the implementation of the discriminant functions into a decision tree that constitutes a new program called FirstEF. By using different models to predict CpG-related and non-CpG-related first exons, we showed by cross-validation that the program could predict 86% of the first exons with 17% false positives. We also demonstrated the prediction accuracy of FirstEF at the genome level by applying it to the finished sequences of human chromosomes 21 and 22 as well as by comparing the predictions with the locations of the experimentally verified first exons. Finally, we present the analysis of the predicted first exons for all of the 24 chromosomes of the human genome.

Item Type: Paper
Uncontrolled Keywords: CPG ISLANDS DISCRIMINANT-ANALYSIS DNA-SEQUENCE BIOLOGY REGIONS GENES
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: December 2001
Date Deposited: 22 Jan 2014 20:07
Last Modified: 22 Jan 2014 20:07
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29228

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