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

Ramana V. Davuluri1

1 Ohio State University, Columbus, Ohio
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 4.7
DOI:  10.1002/0471250953.bi0407s01
Online Posting Date:  May, 2003
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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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Table of Contents

  • 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

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.
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