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Suite of packages for sequencing, searching, etc. written in C: Linux, macOS, Unix, Windows [4] GPL and LGPL: Collaborative project Galaxy: Scientific workflow and data integration system Unix-like: Academic Free: Collaborative project GenePattern: Scientific workflow system that provides access to hundreds of genomic analysis tools
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 ...
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 ...
REAL is an efficient, accurate, and sensitive tool for aligning short reads obtained from next-generation sequencing. The programme can handle an enormous amount of single-end reads generated by the next-generation Illumina/Solexa Genome Analyzer. cREAL is a simple extension of REAL for aligning short reads obtained from next-generation ...
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. [3] The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. As of 2017, the Genome Biology paper describing the original Bowtie method has been cited more than ...
The package contains additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation, and other components for data analysis. The latest version of the software was released in 2021. [3]
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]