ArticleBMC bioinformatics2019
Computational discovery and annotation of conserved small open reading frames in fungal genomes.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 31 citations in OpenAlex.
- Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum.BMC biology · 2026Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Discovering the hidden function in fungal genomes.Nature communications · 2024Review
- Transposon mutagenesis screen ineLife · 2024Article
- Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes).mSystems · 2024Article
- Exploring microproteins from various model organisms using the mip-mining database.BMC genomics · 2023Article
- Pervasive translation of small open reading frames in plant long non-coding RNAs.Frontiers in plant science · 2022Review
- A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.BMC genomics · 2020Article
- Accurate detection of short and long active ORFs using Ribo-seq data.Bioinformatics (Oxford, England) · 2020Article
- AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.Bioinformatics (Oxford, England) · 2020Article
- 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
- Proteomic Detection and Validation of Translated Small Open Reading Frames.Current protocols in chemical biology · 2019Article
- APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018.BMC genomics · 2019Article
- OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.Evolutionary bioinformatics online · 2019Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundSmall open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotated. For many genomes, a second round of sORF targeted gene prediction can complement the existing annotation. In this study, we specifically targeted the identification of ORFs encoding for 80 amino acid residues or less from 31 fungal genomes. We then compared the predicted sORFs and analysed those that are highly conserved among the genomes.
resultsA first set of sORFs was identified from existing annotations that fitted the maximum of 80 residues criterion. A second set was predicted using parameters that specifically searched for ORF candidates of 80 codons or less in the exonic, intronic and intergenic sequences of the subject genomes. A total of 1986 conserved sORFs were predicted and characterized.
conclusionsIt is evident that numerous open reading frames that could potentially encode for polypeptides consisting of 80 amino acid residues or less are overlooked during standard gene prediction and annotation. From our results, additional targeted reannotation of genomes is clearly able to complement standard genome annotation to identify sORFs. Due to the lack of, and limitations with experimental validation, we propose that a simple conservation analysis can provide an acceptable means of ensuring that the predicted sORFs are sufficiently clear of gene prediction artefacts.
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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.