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Gene Structure Prediction Tools

  • Glimmer and GlimmerM
A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The decision about what gene model is best is a combination of the strength of the splice sites and the score of the exons generated by an interpolated Markov model (IMM). The system has been trained for Arabidopsis thaliana, Oryza sativa (rice), and Plasmodium falciparum (the malaria parasite), and should work well on closely related organisms.

  • Grail and GrailExp
It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program.

GENSCAN, a computer program for gene identification, uses this model. GENSCAN determines various parameters of the model to get meaningful results. The program uses a training set of 238 multi-exon genes and 142 single-exon genes. These are completely sequenced genes from GenBank. On whole, the training set consists of about 2.5 million base pairs.