ArticleBioinformatics (Oxford, England)2013
cisExpress: motif detection in DNA sequences.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- DNA methylation changes in clonally propagated oil palm.Plant cell reports · 2020Article
- Characterization of the mitochondrial genome of the MAX1 type of cytoplasmic male-sterile sunflower.BMC plant biology · 2019Article
- Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation.Molecular neurobiology · 2018Article
- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
- Article
- Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis.Experimental & molecular medicine · 2016Article
- Nucleotide diversity analysis highlights functionally important genomic regions.Scientific reports · 2016Article
- iRegulon: from a gene list to a gene regulatory network using large motif and track collections.PLoS computational biology · 2014Article
- 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.Database : the journal of biological databases and curation · 2014Article
- NPEST: a nonparametric method and a database for transcription start site prediction.Quantitative biology (Beijing, China) · 2013Article
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5 authors.
Funding
Abstract
motivationOne of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities between the promoters of similarly expressed genes. This new tool, cisExpress, is especially designed for use with large datasets, such as those generated by publicly accessible whole genome and transcriptome projects. cisExpress uses a task farming algorithm to exploit all available computational cores within a shared memory node. We demonstrate the robust nature and validity of the proposed method. It is applicable for use with a wide range of genomic databases for any species of interest. AVAILABILITY: cisExpress is available at www.cisexpress.org.
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