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Gene Prediction. Chengwei Luo, Amanda McCook, Nadeem Bulsara, Phillip Lee, Neha Gupta, and Divya Anjan Kumar. Gene Prediction. Introduction Protein-coding gene prediction RNA gene prediction Modification and finishing Project schema. Gene Prediction. Introduction
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Gene Prediction • Chengwei Luo, Amanda McCook, Nadeem Bulsara, • Phillip Lee, Neha Gupta, and Divya Anjan Kumar
Gene Prediction • Introduction • Protein-coding gene prediction • RNA gene prediction • Modification and finishing • Project schema
Gene Prediction • Introduction • Protein-coding gene prediction • RNA gene prediction • Modification and finishing • Project schema
Why gene prediction? experimental way?
Why gene prediction? Exponential growth of sequences New sequencing technology Metagenomics: ~1% grow in lab
How to do it? It is a complicated task, let’s break it into parts
How to do it? It is a complicated task, let’s break it into parts Genome
How to do it? It is a complicated task, let’s break it into parts Genome
How to do it? Protein-coding gene prediction Homology Search Phillip Lee & Divya Anjan Kumar ab initio approach Nadeem Bulsara & Neha Gupta
How to do it? RNA gene prediction Amanda McCook & Chengwei Luo tRNA rRNA sRNA
Homology Search is not Enough! Biased and incomplete Database sequenced genomes are not evenly distributed on the tree of life, and does not reflect the diversity accordingly either.
Usually Used Tools GeneMark Glimmer EasyGene PRODIGAL
PRODIGALProkaryotic Dynamic Programming Gene Finding Algorithm Developed at Oak Ridge National Laboratory and the University of Tennessee
EasyGene Developed at University of Copenhagen Statistical significance is the measure for gene prediction.
