ArticleNucleic acids research2009
Non-coding RNA annotation of the genome of Trichoplax adhaerens.
Article in Nucleic acids research, 2009. 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, 65 citations in OpenAlex.
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- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
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- A comprehensive comparison of general RNA-RNA interaction prediction methods.Nucleic acids research · 2016Article
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- Dissemination of 6S RNA among bacteria.RNA biology · 2014Article
- ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.BMC bioinformatics · 2014Article
- Bioinformatics of prokaryotic RNAs.RNA biology · 2014Review
- Computational approaches in detecting non- coding RNA.Current genomics · 2013Article
- Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants.Molecular biology and evolution · 2013Article
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.Algorithms for molecular biology : AMB · 2013Article
- MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi.BMC genomics · 2012Article
- Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?RNA biology · 2012Article
- Searching for non-coding RNAs in genomic sequences using ncRNAscout.Genomics, proteomics & bioinformatics · 2012Article
- Evolution of the let-7 microRNA family.RNA biology · 2012Article
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.
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