ArticleBioinformatics (Oxford, England)2021
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.
Article in Bioinformatics (Oxford, England), 2021. 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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16 citing papers in PubMed.
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- Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.Communications biology · 2025Article
- Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.bioRxiv : the preprint server for biology · 2024Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk.Cell genomics · 2024Article
- Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease.PLoS computational biology · 2024Article
- Regulatory activity is the default DNA state in eukaryotes.Nature structural & molecular biology · 2024Article
- Design and deep learning of synthetic B-cell-specific promoters.Nucleic acids research · 2023Article
- Transcriptional reprogramming by mutated IRF4 in lymphoma.Nature communications · 2023Article
- ExplaiNN: interpretable and transparent neural networks for genomics.Genome biology · 2023Article
- A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.Science immunology · 2023Article
- Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck.Biology · 2022Article
- Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
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4 authors.
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Abstract
motivationAccurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.
resultsWe developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five different bin sizes to generate appropriate genomic background sequences. AVAILABILITY AND IMPLEMENTATION: BiasAway source code is freely available from Bitbucket (https://bitbucket.org/CBGR/biasaway) and can be easily installed using bioconda or pip. The web server is available at https://biasaway.uio.no and a detailed documentation is available at https://biasaway.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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