ArticleNucleic acids research2014
Realistic artificial DNA sequences as negative controls for computational genomics.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Vole genomics links determinate and indeterminate growth of teeth.bioRxiv : the preprint server for biology · 2024Article
- Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants.Cell genomics · 2024Article
- WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences.Bioinformatics advances · 2024Article
- Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity.Nature communications · 2023Article
- i4mC-GRU: Identifying DNA NComputational and structural biotechnology journal · 2023Article
- Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer.JCO precision oncology · 2022Article
- Methodologies for theGenes · 2022Review
- Comparison of machine learning and deep learning techniques in promoter prediction across diverse species.PeerJ. Computer science · 2021Article
- RepeatModeler2 for automated genomic discovery of transposable element families.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC bioinformatics · 2019Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Assembly of the Mitochondrial Genome in the Campanulaceae Family Using Illumina Low-Coverage Sequencing.Genes · 2018Article
- An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.Molecular biology and evolution · 2018Article
- A systematic, large-scale comparison of transcription factor binding site models.BMC genomics · 2016Article
- Trimming of sequence reads alters RNA-Seq gene expression estimates.BMC bioinformatics · 2016Article
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Authors and funding
4 authors.
Funding
Abstract
A common practice in computational genomic analysis is to use a set of 'background' sequences as negative controls for evaluating the false-positive rates of prediction tools, such as gene identification programs and algorithms for detection of cis-regulatory elements. Such 'background' sequences are generally taken from regions of the genome presumed to be intergenic, or generated synthetically by 'shuffling' real sequences. This last method can lead to underestimation of false-positive rates. We developed a new method for generating artificial sequences that are modeled after real intergenic sequences in terms of composition, complexity and interspersed repeat content. These artificial sequences can serve as an inexhaustible source of high-quality negative controls. We used artificial sequences to evaluate the false-positive rates of a set of programs for detecting interspersed repeats, ab initio prediction of coding genes, transcribed regions and non-coding genes. We found that RepeatMasker is more accurate than PClouds, Augustus has the lowest false-positive rate of the coding gene prediction programs tested, and Infernal has a low false-positive rate for non-coding gene detection. A web service, source code and the models for human and many other species are freely available at http://repeatmasker.org/garlic/.
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