ArticleBioinformatics (Oxford, England)2012
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice.Scientific reports · 2019Article
- A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model.BioMed research international · 2017Article
- Article
- High resolution mapping of enhancer-promoter interactions.PloS one · 2015Article
- Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.Nucleic acids research · 2013Article
- Article
- RFECS: a random-forest based algorithm for enhancer identification from chromatin state.PLoS computational biology · 2013Article
- CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.BMC genomics · 2012Article
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7 authors.
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Abstract
motivationThe prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.
resultsWe have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith-Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.
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