ArticleBMC bioinformatics2010
MapMi: automated mapping of microRNA loci.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The first chromosome-level cubozoan genome differentiates unique and common features in different cnidarian lineages.BMC biology · 2026Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- InsectBase 2.0: a comprehensive gene resource for insects.Nucleic acids research · 2022Article
- RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.BMC bioinformatics · 2021Article
- Large-Scale Annotation and Evolution Analysis of MiRNA in Insects.Genome biology and evolution · 2021Article
- Identification and Analysis of MicroRNAs Associated with Wing Polyphenism in the Brown Planthopper,International journal of molecular sciences · 2020Article
- Small RNAs in eucaryotes: new clues for amplifying microRNA benefits.Cell & bioscience · 2020Review
- A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance.Nature communications · 2019Article
- MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions.Scientific reports · 2019Article
- The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum.BMC genomics · 2018Article
- Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.Genome research · 2017Article
- miRNA profiling of human naive CD4 T cells links miR-34c-5p to cell activation and HIV replication.The EMBO journal · 2017Article
- The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle.Scientific reports · 2016Article
- Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.Genome biology · 2015Article
- Evidence for the expression of abundant microRNAs in the locust genome.Scientific reports · 2015Article
- The EMBL-EBI bioinformatics web and programmatic tools framework.Nucleic acids research · 2015Article
- MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi.Insect molecular biology · 2015Article
- microRNAs of parasitic helminths - Identification, characterization and potential as drug targets.International journal for parasitology. Drugs and drug resistance · 2014Review
- Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.PloS one · 2014Article
- CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.RNA biology · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. However, miRBase focuses on those species for which miRNAs have been directly confirmed. Secondly, specific miRNAs or their loci are sometimes not annotated even in well-covered species. We sought to address this problem by developing a computational system for automated mapping of miRNAs within and across species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. Our primary goal is not the discovery of novel miRNAs but the mapping of validated miRNAs in one species to their most likely orthologues in other species.
resultsWe present MapMi, a computational system for automated miRNA mapping across and within species. This method has a sensitivity of 92.20% and a specificity of 97.73%. Using the latest release (v14) of miRBase, we obtained 10,944 unannotated potential miRNAs when MapMi was applied to all 21 species in Ensembl Metazoa release 2 and 46 species from Ensembl release 55.
conclusionsThe pipeline and an associated web-server for mapping miRNAs are freely available on http://www.ebi.ac.uk/enright-srv/MapMi/. In addition precomputed miRNA mappings of miRBase miRNAs across a large number of species are provided.
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