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Abstract MotivationThe availability of numerous ChIP-seq datasets for transcription factors (TF) has provided an unprecedented opportunity to identify all TF binding sites in genomes. However, the progress has been hindered by the lack of a highly efficient and accurate tool to find not only the target motifs, but also cooperative motifs in very big datasets. ResultsWe herein present an ultrafast and accurate motif-finding algorithm, ProSampler, based on a novel numeration method and Gibbs sampler. ProSampler runs orders of magnitude faster than the fastest existing tools while often more accurately identifying motifs of both the target TFs and cooperators. Thus, ProSampler can greatly facilitate the efforts to identify the entire cis-regulatory code in genomes. Availability and implementationSource code and binaries are freely available for download at https://github.com/zhengchangsulab/prosampler. It was implemented in C++ and supported on Linux, macOS and MS Windows platforms. Supplementary informationSupplementary materials are available at Bioinformatics online.
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CREPE: a Shiny app for transcription factor cataloguing
Abstract SummaryTranscription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unraveling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE was benchmarked against curated human TF datasets. Next, we use CREPE to explore the TF repertoires of Heliconius erato and Heliconius melpomene butterflies. Availability and implementationCREPE is available as a Shiny app package available at GitHub (github.com/dirostri/CREPE). Supplementary informationSupplementary data are available at Bioinformatics Advances online.
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- Award ID(s):
- 1736026
- PAR ID:
- 10411746
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics Advances
- Volume:
- 3
- Issue:
- 1
- ISSN:
- 2635-0041
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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