ArticleBMC bioinformatics2020
SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 7 citations in OpenAlex.
- Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms.Molecular biology and evolution · 2025Article
- SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads.Briefings in bioinformatics · 2025Article
- A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa.Open biology · 2022Article
- SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data.BMC bioinformatics · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundSpliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced.
resultsIn this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing.
conclusionsSLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.
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Registered trials
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