ArticleGenomics, proteomics & bioinformatics2018
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs.
Article in Genomics, proteomics & bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers.
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Who cites it
109 citing papers in PubMed.
- Paternal cytokine administration alters sperm small ncRNAs and offspring brain and behavior.Molecular psychiatry · 2026Article
- qMAP decodes RNA fragmentation dynamics in development and disease.Molecular systems biology · 2026Article
- Updated guide to RNA quantification by RNA sequencing and reverse transcription-qPCR.Molecules and cells · 2026Article
- A modular class-aware workflow for small RNA sequencing analysis using mouse sperm as a case study.Epigenomics · 2026Article
- PANDORA-seq reveals human sperm sncRNA signature endowed with sperm quality assessment.Genes & diseases · 2026Article
- Ribonuclease DIS3 delays aging and senescence by generating tRNA halves.Nature communications · 2026Article
- Environmentally-induced sperm RNAs shape placentation and fetal growth.Research square · 2026Article
- Circulating non-canonical small non-coding RNAs as novel diagnostic biomarkers for tuberculosis.Microbiology spectrum · 2026Article
- Alterations in MicroRNA and Cytokine Expressions in Placental and Amniotic Tissues of COVID-19 Affected Pregnant Women.The Kaohsiung journal of medical sciences · 2026Article
- Endogenous and Exogenous Small RNA Signatures as Novel Tools for Postmortem Interval Determination.Biomolecules · 2026Article
- FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.NAR genomics and bioinformatics · 2026Article
- Dissecting the small RNA code of inflammatory bowel disease.Molecular medicine (Cambridge, Mass.) · 2026Article
- Paternal Microplastic Exposure Alters Sperm Small Noncoding RNAs and Affects Offspring Metabolic Health in Mice.Journal of the Endocrine Society · 2026Article
- Conserved shifts in sperm small non-coding RNA profiles during mouse and human aging.The EMBO journal · 2026Article
- A cholesterol-responsive hepatic tRNA-derived small RNA regulates cholesterol homeostasis and atherosclerosis development.Nature communications · 2025Article
- Vinclozolin and MEHP disrupt piRNA and miRNA expression and increase apoptosis in embryonic mouse ovaries.Scientific reports · 2025Article
- FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs.Bioinformatics (Oxford, England) · 2025Article
- New insights into temperature-impacted mycovirus-fungus interactions regulated by a microRNA inJournal of virology · 2025Article
- Combinatorial tagging generates a multi-purpose knock-in mouse model revealing phase separation-dependent germ granules in RNA homeostasis and germline development.Cell death and differentiation · 2025Article
- Transfer RNA-derived small RNAs (tsRNAs): A rising star in liquid biopsy.Genes & diseases · 2025Review
49 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users' input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.
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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.