Application of FirstEF to Find Promoters and First Exons in the Human Genome

互联网2013-12-31

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Abstract
Table of Contents
Figures
Literature Cited

Abstract

Predicting first exons and promoters is an important part of gene finding in DNA sequence analysis. This unit presents FirstEF as a method for predicting the first exons and promoters. A combines FirstEF predictions with other information such as cDNA/EST matches.

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Basic Protocol 1: Using Web‐Based FirstEF to Predict Promoters and First Exons
Alternate Protocol 1: Using Local FirstEF to Predict Promoters and First Exons
Support Protocol 1: Combining FirstEF Predictions with Other Annotations
Guidelines for Understanding Results
Commentary
Literature Cited
Figures
Tables

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Materials

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Figures

Figure 4.7.1 The screen shot of the FirstEF Web page (see Internet Resources). The README file, available with the downloaded version, gives a brief description of how to use FirstEF. Examples of human genomic sequences analyzed by FirstEF are presented at the Web site. Preliminary annotations of the human genome can also be accessed from this Web site.

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Figure 4.7.2 Screen shot of FirstEF output of Example 1 with default cut‐off values for P(exon) , P(promoter) , and P(donor) . For each sequence in the input file, FirstEF presents predictions on direct and complementary strands separately. Sequence header follows the symbol for each block of predictions. The line immediately following gives the strand information for the predictions which follow. Descriptions of each column are given in Table .

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Figure 4.7.3 Part of the annotations for Example 1 (from 1 to 60000 bp) obtained by following the steps described (see ). Exons+ and Exons‐ indicate the predicted first exons on direct and complementary strands, respectively. The exon with symbol i.j represents j^th ‐ranked first exon in the i^th cluster. AK027391 represents the transcript mapped to the exons complement (14015..12633, 11583..10224). Refer to Table for this and the exon coordinates of other mapped cDNA/ESTs. For the coordinates of the first exons and CpG windows refer to Figure .

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Videos

Literature Cited

	Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78‐94.
	Davuluri, R.V., Grosse, I., and Zhang, M.Q. 2001. Computational identification of first exons and promoters in human genome. Nature Gen. 29:412‐417.
	Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8:967‐974.
	Gardiner‐Garden, M. and Frommer, M. 1987. CpG islands in vertebrate genomes. J. Mol. Biol. 196:261‐276.
	Ioshikhes, I. and Zhang, M.Q. 2000. Large‐scale human promoter mapping using CpG islands. Nature Gen. 26:61‐63.
	Scherf, M., Klingenhoff, A., and Werner, T. 2000. Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach. J. Mol. Biol. 297:599‐606.
	Zhang, M.Q. 1997. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl. Acad. Sci. U.S.A. 94:565‐568.
Key References
	Davuluri et al., 2001. See above.
	The algorithm details of FirstEF and its accuracy in predicting first exons and promoters using a test set of experimentally known first exons is described. The performance of FirstEF over a large genomic regions (human chromosomes 21 and 22) is also discussed.
	Davuluri, R.V., Grosse, I., and Zhang, M.Q.,
	FirstEF has been used to perform an initial computational annotation of the promoters and the first exons for all 24 human chromosomes. Visit http://genemap.med.ohio‐state.edu for accessing the annotations.
Internet Resources
	http://rulai.cshl.org/tools/FirstEF
	The FirstEF Web‐based version.
	http://genemap.med.ohio‐state.edu
	The Bioinformatics Unit of the Human Cancer Genetics Program at The Ohio State University. The First Exon genome browser is available from this site.
	http://www.ncbi.nih.gov/BLAST
	The BLAST and MEGABLAST homepage at the NCBI. See UNITS & for more information.
	http://pbil.univ‐lyon1.fr/sim4.html
	The SIM4 Web site. See Florea et al. () for more information.
	http://genes.mit.edu/GENSCAN.html
	The GENSCAN server at MIT.
	http://www.cshl.edu/mzhanglab or http://rulai.cshl.edu
	The Zhang Laboratory Computational Biology and Bioinformatics website. A link to MZEF is available through this site.
	http://www.wormbase.org/db/seq/frend
	The Sequence Feature Renderer home page. Figure was created using this tool.