ArticleNucleic acids research2011
BlastR--fast and accurate database searches for non-coding RNAs.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genome-wide analysis of mRNA and lncRNA expression and mitochondrial genome sequencing provide insights into the mechanisms underlying a novel cytoplasmic male sterility system, BVRC-CMS96, in Brassicarapa.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics.BMC bioinformatics · 2018Article
- High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.Nature genetics · 2017Article
- FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.Nucleic acids research · 2017Article
- In silico discovery and modeling of non-coding RNA structure in viruses.Methods (San Diego, Calif.) · 2015Review
- Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs.Nucleic acids research · 2015Article
- Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.Bioinformatics (Oxford, England) · 2014Article
- Bioinformatics of prokaryotic RNAs.RNA biology · 2014Review
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.Annual review of biophysics · 2014Review
- Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.Nucleic acids research · 2013Article
- Detecting and comparing non-coding RNAs in the high-throughput era.International journal of molecular sciences · 2013Review
- Review
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.Algorithms for molecular biology : AMB · 2013Article
- Use of ChIP-Seq data for the design of a multiple promoter-alignment method.Nucleic acids research · 2012Article
- Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).PloS one · 2012Article
- piRNAs and Their Functions in the Brain.International journal of human geneticsArticle
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.
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Registered trials
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.