De novo motif discovery software tools | ChIP sequencing data analysis
De novo motif discovery is a difficult computational task. Historically, dedicated algorithms always reported a high percentage of false positives. Their performance did not improve considerably even after they adapted to handle large amounts of chromatin immunoprecipitation sequencing (ChIP-Seq) data.
Provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters.
Performs peak finding and downstream data analysis for next-generation sequencing analysis. HOMER affords several tools and methods to make use of ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and other types of functional genomics sequencing data sets. This software offers support to UCSC visualization, peaks annotation, quantification of transcripts and repeats or differential features, enrichment and expression.
Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.
A web-based tool for analyzing motifs in large DNA or RNA data sets. MEME-ChIP can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP is part of the MEME Suite online platform.
A motif discovery algorithm specifically designed to find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very large ChIP-seq datasets in minutes. DREME is available as part of the MEME Suite of motif-based sequence analysis tools.
Offers an approach for motif discovery based on a Bayesian approach. BAMM!motif is an application that exploits Bayesian Markov Models (BaMMs) to perform its predictions. It consists of four distinct modules allowing users to: (i) investigate nucleotide sequence to determine high-order motifs; (ii) explore model repositories with a feature for searching given motifs against a pre-computed database; and (iii) detect motifs occurrences from sequences.
Identifies known or user-provided motifs that show a significant preference for particular locations in your nucleotide sequences. CentriMo can also show if the local enrichment is significant relative to control sequences. It is part of the MEME Suite online platform.