Transcription factor binding site detection software tools | Genome annotation
Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal.
Analyzes data generated by short read sequencers. MACS is a standalone software dedicated to the forecasting of protein-DNA interaction sites from ChIP-Seq. The application is able to: (i) model the distance d and shifting tags by d/2 to enable the spatial resolution of the predicted sites; (ii) capture local biases in the genome by exploiting a dynamic λ local parameter and (iii) evaluate the false discovery rate (FDR) for each detected peak.
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.
Allows identification of transcription factor binding sites (TFBS) in nucleotide sequences, using a large library of matrix descriptions. MatInspector is a TFBS prediction programs that uses the information of core positions, nucleotide distribution matrix and Ci-vector to scan sequences of unlimited length for pattern matches. The software can find the potential binding sites of various activators and repressors that bind to specific DNA regulatory sequences. It is part of the Genomatix Software Suite.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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.
Offers a component-based architecture that allows users to add new functionality in the form of plug-in modules. geWorkbench includes many computational resources permitting to delete many steps that require programming skills. It simplifies the utilization of multi-module analysis pipelines. The tool’s modules consist of wrapped versions of pre-existing third-party software tools.
A comparative tool for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. rVISTA analysis proceeds in four main steps: (i) detect TFBS matches in each individual sequence using PWMs from the TRANSFAC database, (ii) identify pairs of locally aligned TFBSs, (iii) select TFBSs present in regions of high DNA conservation and (iv) create a graphical display that dynamically overlays individual or clustered TFBSs with the conservation profile of the genomic locus. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences.