alexa Automatic annotation of eukaryotic genes, pseudogenes and promoters.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Data Mining in Genomics & Proteomics

Author(s): Solovyev V, Kosarev P, Seledsov I, Vorobyev D

Abstract Share this page

Abstract BACKGROUND: The ENCODE gene prediction workshop (EGASP) has been organized to evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the manual and experimental gene annotation of the human genome. We have used Softberry gene finding software to predict genes, pseudogenes and promoters in 44 selected ENCODE sequences representing approximately 1\% (30 Mb) of the human genome. Predictions of gene finding programs were evaluated in terms of their ability to reproduce the ENCODE-HAVANA annotation. RESULTS: The Fgenesh++ gene prediction pipeline can identify 91\% of coding nucleotides with a specificity of 90\%. Our automatic pseudogene finder (PSF program) found 90\% of the manually annotated pseudogenes and some new ones. The Fprom promoter prediction program identifies 80\% of TATA promoters sequences with one false positive prediction per 2,000 base-pairs (bp) and 50\% of TATA-less promoters with one false positive prediction per 650 bp. It can be used to identify transcription start sites upstream of annotated coding parts of genes found by gene prediction software. CONCLUSION: We review our software and underlying methods for identifying these three important structural and functional genome components and discuss the accuracy of predictions, recent advances and open problems in annotating genomic sequences. We have demonstrated that our methods can be effectively used for initial automatic annotation of the eukaryotic genome.
This article was published in Genome Biol and referenced in Journal of Data Mining in Genomics & Proteomics

Relevant Expert PPTs

Relevant Speaker PPTs

Recommended Conferences

  • 3rd World Congress on Human Genetics
    August 14-15, 2017 Edinburgh, Scotland
  • 9th International Conference on Bioinformatics
    October 23-24, 2017 Paris, France
  • 9th International Conference and Expo on Proteomics
    October 23-25, 2017 Paris, France

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords