ExtRamp: A novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or the codon adaptation index
Authors: Justin Miller*, Logan Brase*, Perry Ridge
Nucleic Acids Research
Revisions due January, 2019
Nucleic Acids Research has an impact factor of 11.561
Novelty of Approach
-Novel algorithm to extract the ramp sequence from any DNA sequence
-Validate approach by running ExtRamp on 229 742 339 genes across 23 428 species
-Provide options for arithmetic, geometric, and harmonic means
-Validate approach on bulk analysis previously published in Cell
-Assess the expression levels in Drosophila for genes that use ramp sequences
Results
-Fast algorithm (entire species analyzed in seconds)
-Species are currently being reanalyzed using harmonic mean and local codon adaptation instead of species-wide adaptation
Implications
-Ramp sequences have been systematically ignored in many studies.
-Some studies have assumed all genes have ramp sequences
-Codon usage biases vary throughout genes
-Better analyze ribosome spacing and understand cell dynamics
Ramp Sequences in Various Species Partitions
Bulk Ramp Sequence Analysis