gene finding in novel genomes by ian korf n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
“Gene Finding in Novel Genomes” by Ian Korf PowerPoint Presentation
Download Presentation
“Gene Finding in Novel Genomes” by Ian Korf

Loading in 2 Seconds...

play fullscreen
1 / 12

“Gene Finding in Novel Genomes” by Ian Korf - PowerPoint PPT Presentation


  • 86 Views
  • Uploaded on

“Gene Finding in Novel Genomes” by Ian Korf. Presented by: Christine Lee SoCAL BSI 2004. Outline. Background and Motivation Existing gene finder programs Snap as ab initio high performance gene finder Novel genome gene prediction The Data Genome compositional differences

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about '“Gene Finding in Novel Genomes” by Ian Korf' - tahir


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
gene finding in novel genomes by ian korf

“Gene Finding in Novel Genomes” by Ian Korf

Presented by:

Christine Lee

SoCAL BSI 2004

outline
Outline
  • Background and Motivation
  • Existing gene finder programs
  • Snap as ab initio high performance gene finder
  • Novel genome gene prediction
  • The Data
  • Genome compositional differences
  • Parameter estimation in novel genomes
  • Conclusion
background and motivation
Background and motivation
  • Rapid genome sequencing
  • Key task: identification of structure of protein-coding region
  • Ab initio gene prediction
  • Gene finder
  • Annotation of novel genome
  • SNAP & de novo species-specific parameter estimation
existing gene finder programs
Existing gene finder programs
  • Genscan: performs as well as recent gene finders designed for Arabidopsis
  • HMMGene and Genefinder: well-established gene prediction programs for C. elegans
  • Augustus: one of the latest, shown to outperform Genscan, GENIE, and GENEID in Drosophilla
data set
Data Set

Data set characteristics At Arabidopsis thaliana, Ce Caenorhabditis elegans,

Dm Drosophila melanogaster, Os Oryza sativa.

slide10

Performance of foreign and bootstrapped parameters. The bold face values are determined by 5-fold cross-validation

within the same species. At Arabidopsis thaliana, Ce Caenorhabditis elegans, Dm Drosophila melanogaster,

Os Oryza sativa. Sensitivity (NSN) and specificity (NSP) are reported at the nucleotide level. The bootstrapped values

(bottom part of the table) are derived from parameter estimates based on gene predictions and no

actual data. In these experiments, only inter-species gene parameters were used; dashes

represent cells that would contain intra-species predictions.

conclusion and future work
Conclusion and Future Work
  • Feasibility of gene finder as bootstrap predictor
  • Improved results through implementation of advanced statistical methods
  • Apply gene prediction to large genomes