ArticleNucleic acids research2019
ExtRamp: a novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Self-amplifying mRNA vaccine cocktail against Staphylococcus aureus: A multi-epitope immunoinformatics and structural simulation framework.World journal of microbiology & biotechnology · 2026Article
- Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.Genome biology and evolution · 2026Article
- Ramp Sequence May Explain Synonymous Variant Association with Alzheimer's Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA).Biomedicines · 2025Article
- Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (bioRxiv : the preprint server for biology · 2025Article
- TgVax452, an epitope-based candidate vaccine targeting Toxoplasma gondii tachyzoite-specific SAG1-related sequence (SRS) proteins: immunoinformatics, structural simulations and experimental evidence-based approaches.BMC infectious diseases · 2024Article
- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Evidence for selection on SARS-CoV-2 RNA translation revealed by the evolutionary dynamics of mutations in UTRs and CDSs.RNA biology · 2022Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates.Scientific reports · 2021Article
- CUBAP: an interactive web portal for analyzing codon usage biases across populations.Nucleic acids research · 2020Article
- Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes.mSystems · 2020Article
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Authors and funding
3 authors.
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Abstract
Different species, genes, and locations within genes use different codons to fine-tune gene expression. Within genes, the ramp sequence assists in ribosome spacing and decreases downstream collisions by incorporating slowly-translated codons at the beginning of a gene. Although previously reported as occurring in some species, no previous attempt at extracting the ramp sequence from specific genes has been published. We present ExtRamp, a software package that quickly extracts ramp sequences from any species using the tRNA adaptation index or relative codon adaptiveness. Different filters facilitate the analysis of codon efficiency and enable identification of genes with a ramp sequence. We validate the existence of a ramp sequence in most species by running ExtRamp on 229 742 339 genes across 23 428 species. We evaluate differences in reported ramp sequences when we use different parameters. Using the strictest ramp sequence cut-off, we show that across most taxonomic groups, ramp sequences are approximately 20-40 codons long and occur in about 10% of gene sequences. We also show that in Drosophila melanogaster as gene expression increases, a higher proportion of genes have ramp sequences. We provide a framework for performing this analysis on other species. ExtRamp is freely available at https://github.com/ridgelab/ExtRamp.
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