Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data
VV Raditsa, AV Tsukanov, AG Bogomolov, VG Levitsky - bioRxiv, 2024 - biorxiv.org
Efficient de novo motif discovery from the results of wide-genome mapping of transcription
factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide …
factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide …
Ultra-fast and accurate motif finding in large ChIP-seq datasets reveals transcription factor binding patterns
The availability of a large volume of chromatin immunoprecipitation followed by sequencing
(ChIP-seq) datasets for various transcription factors (TF) has provided an unprecedented …
(ChIP-seq) datasets for various transcription factors (TF) has provided an unprecedented …
Evidence-ranked motif identification
Abstract cERMIT is a computationally efficient motif discovery tool based on analyzing
genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate …
genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate …
RSAT:: Plants: Motif discovery in ChIP-Seq peaks of plant genomes
JA Castro-Mondragon, C Rioualen… - … Promoters: Methods and …, 2016 - Springer
In this protocol, we explain how to run ab initio motif discovery in order to gather putative
transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP …
transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP …
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling
Motivation The discovery of sequence motifs mediating DNA-protein binding usually implies
the determination of binding sites using high-throughput sequencing and peak calling. The …
the determination of binding sites using high-throughput sequencing and peak calling. The …
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery
Motivation The availability of numerous ChIP-seq datasets for transcription factors (TF) has
provided an unprecedented opportunity to identify all TF binding sites in genomes. However …
provided an unprecedented opportunity to identify all TF binding sites in genomes. However …
Factorbook Motif Pipeline: A de novo motif discovery and filtering web server for ChIP-seq peaks
High-throughput sequencing technologies such as ChIP-seq have deepened our
understanding in many biological processes. De novo motif search is one of the key …
understanding in many biological processes. De novo motif search is one of the key …
AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses
Motif discovery is essential for deciphering regulatory codes from high throughput genomic
data, such as those from ChIP-chip/seq experiments. However, there remains a lack of …
data, such as those from ChIP-chip/seq experiments. However, there remains a lack of …
Differential motif enrichment analysis of paired ChIP-seq experiments
Background Motif enrichment analysis of transcription factor ChIP-seq data can help identify
transcription factors that cooperate or compete. Previously, little attention has been given to …
transcription factors that cooperate or compete. Previously, little attention has been given to …
Deep and wide digging for binding motifs in ChIP-Seq data
ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of
thousands of DNA segments with base-specific coverage values. We present a new version …
thousands of DNA segments with base-specific coverage values. We present a new version …