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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.
It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory sites. [10] In the context of ChIP-exo, this process is known as 'peak-pair calling'. [11] Differential peak calling is about identifying significant differences in two ChIP-seq signals. One can distinguish between one ...
Results of differential expression analysis can be integrated with ChIP-Seq data to build average tag density profiles and heat maps. The package makes use of several tools open source tools including STAR and DESeq. See also. [72] Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for ...
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 ...
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 company also manufactured machinery for high speed analysis of biological samples, and its GeneChip Operating Software as a system for managing Affymetrix microarray data. Affymetix's competitors in the DNA Microarray business include Illumina , GE Healthcare , Applied Biosystems , Beckman Coulter , Eppendorf Biochip Systems, and Agilent .
Hi-C uses high-throughput sequencing to find the nucleotide sequence of fragments [2] [22] and uses paired end sequencing, which retrieves a short sequence from each end of each ligated fragment. As such, for a given ligated fragment, the two sequences obtained should represent two different restriction fragments that were ligated together in ...
DNAnexus is an American company that provides a cloud-based data analysis and management platform for DNA sequence data.It is based in Mountain View, California, and was founded in 2009 by Stanford University professors Serafim Batzoglou and Arend Sidow and Stanford computer scientist Andreas Sundquist.