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Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A phylogeny-based comprehensive database of plant transcription associated proteins.

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• SciCrunch
• 13 years ago - by Anonymous

A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula.

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• SciCrunch
• 13 years ago - by Anonymous

A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

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• SciCrunch
• 13 years ago - by Anonymous

Software for inferring nucleosome positions with their histone mark annotation from ChIP data. It is a versatile tool that can be used to predict positioned nucleosomes from one or multiple ChIP-seq bam files and it can be also used in conjunction with a control experiment.

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• SciCrunch
• 13 years ago - by Anonymous

An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates.

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• SciCrunch
• 13 years ago - by Anonymous

An online server that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy of predition.

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• SciCrunch
• 13 years ago - by Anonymous

A multithreaded Java application for finding positioned nucleosomes from sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.

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• SciCrunch
• 13 years ago - by Anonymous

A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6

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• SciCrunch
• 13 years ago - by Anonymous

Software for Transcription Factor Flexible Models (TFFMs) that represent Transcription Factor Binding Sites (TFBSs) and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and variable length motifs within a single dedicated framework.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A Software program for Predicting Transcription Factor Binding Sites.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool that predicts motifs in full-size peak sets. It performs all steps from motif discovery to visualization of the predicted sites in genome browsers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

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• SciCrunch
• 13 years ago - by Anonymous

An integrated web tool for transcription factor binding site search and visualization. Both the Python Scripts for Offline Scanning and the Python implementation of the LASAGNA algorithm are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

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• SciCrunch
• 13 years ago - by Anonymous

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

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• SciCrunch
• 13 years ago - by Anonymous

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

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• SciCrunch
• 13 years ago - by Anonymous