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Central Motif Enrichment Analysis (CentriMo) is a tool for inferring direct DNA binding from ChIP-seq data. CentriMo is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. CentriMo takes a ...
GeneProf database and analysis tool: GeneProf is a freely accessible, easy-to-use analysis environment for ChIP-seq and RNA-seq data and comes with a large database of ready-analysed public experiments, e.g. for transcription factor binding and histone modifications.
GenePattern is a freely available online platform that provides access to RNA-Seq analysis methods without the need for programming. GeneProf Freely accessible, easy to use analysis pipelines for RNA-seq and ChIP-seq experiments. GREIN is an interactive web platform for re-processing and re-analyzing GEO RNA-seq data. GREIN is powered by the ...
Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOS: GPL: BGI: Staden Package: Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. Linux, macOS, Windows: BSD: Wellcome Trust Sanger Institute, Medical Research Council
Accurately performs gapped alignment of sequence data obtained from next-generation sequencing machines (specifically of Solexa-Illumina) back to a genome of any size. Includes adaptor trimming, SNP calling and Bisulfite sequence analysis. Yes, also supports Illumina *_int.txt and *_prb.txt files with all 4 quality scores for each base
The list of bioinformatics software tools can be split up according to the license used: List of proprietary bioinformatics software; List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software
Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points. [13]
ChIP has also been applied for genome-wide analysis by combining with microarray technology (ChIP-on-chip) or second-generation DNA-sequencing technology (Chip-Sequencing). ChIP can also combine with paired-end tags sequencing in Chromatin Interaction Analysis using Paired End Tag sequencing (ChIA-PET), a technique developed for large-scale, de ...