ArticleBioinformatics (Oxford, England)2020
Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity.Computational and structural biotechnology journal · 2023Article
- Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures.Journal of biomedical science · 2022Review
- The role of micropeptides in biology.Cellular and molecular life sciences : CMLS · 2021Review
- Identification of Non-Canonical Translation Products inFrontiers in genetics · 2021Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationShort bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance.
resultsAnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes. AVAILABILITY AND IMPLEMENTATION: AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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