ArticleBMC bioinformatics2014
uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Recent advances in improving yield and immunity through transcription factor engineering.Journal of integrative plant biology · 2025Review
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Emerging role of endogenous peptides encoded by non-coding RNAs in cancer biology.Non-coding RNA research · 2025Review
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Review
- A survey of experimental and computational identification of small proteins.Briefings in bioinformatics · 2024Review
- Review
- Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.International journal of molecular sciences · 2023Review
- Review
- csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames.Briefings in bioinformatics · 2022Article
- Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures.Journal of biomedical science · 2022Review
- Small open reading frames in plant research: from prediction to functional characterization.3 Biotech · 2022Review
- Pervasive translation of small open reading frames in plant long non-coding RNAs.Frontiers in plant science · 2022Review
- The role of micropeptides in biology.Cellular and molecular life sciences : CMLS · 2021Review
- OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques.Database : the journal of biological databases and curation · 2020Article
- MiPepid: MicroPeptide identification tool using machine learning.BMC bioinformatics · 2019Article
- Quality and quantity control of gene expression by nonsense-mediated mRNA decay.Nature reviews. Molecular cell biology · 2019Review
- Article
- Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs inRNA (New York, N.Y.) · 2019Article
- Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics.Frontiers in genetics · 2018Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral small open reading frames located within the 5' untranslated regions of mRNAs have recently been shown to be translated. In humans, about 50% of mRNAs contain at least one upstream open reading frame representing a large resource of coding potential. We propose that some upstream open reading frames encode peptides that are functional and contribute to proteome complexity in humans and other organisms. We use the term uPEPs to describe peptides encoded by upstream open reading frames.
resultsWe have developed an online tool, termed uPEPperoni, to facilitate the identification of putative bioactive peptides. uPEPperoni detects conserved upstream open reading frames in eukaryotic transcripts by comparing query nucleotide sequences against mRNA sequences within the NCBI RefSeq database. The algorithm first locates the main coding sequence and then searches for open reading frames 5' to the main start codon which are subsequently analysed for conservation. uPEPperoni also determines the substitution frequency for both the upstream open reading frames and the main coding sequence. In addition, the uPEPperoni tool produces sequence identity heatmaps which allow rapid visual inspection of conserved regions in paired mRNAs.
conclusionsuPEPperoni features user-nominated settings including, nucleotide match/mismatch, gap penalties, Ka/Ks ratios and output mode. The heatmap output shows levels of identity between any two sequences and provides easy recognition of conserved regions. Furthermore, this web tool allows comparison of evolutionary pressures acting on the upstream open reading frame against other regions of the mRNA. Additionally, the heatmap web applet can also be used to visualise the degree of conservation in any pair of sequences. uPEPperoni is freely available on an interactive web server at http://upep-scmb.biosci.uq.edu.au.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.