fasta_to_raw
ChIP-based identifcation of TF binding sites
Install
- All systems
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curl cmd.cat/fasta_to_raw.sh
- Debian
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apt-get install pscan-chip - Ubuntu
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apt-get install pscan-chip - Kali Linux
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apt-get install pscan-chip - Windows (WSL2)
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sudo apt-get updatesudo apt-get install pscan-chip - Dockerfile
- dockerfile.run/fasta_to_raw
pscan-chip
ChIP-based identifcation of TF binding sites
The regions on genomic DNA juxtaposed to regions that code for RNA or protein are known to feature many short regions to which proteins bind that are a requirement for the gene to be read out. These so called transcription factors (TFs) are proteins themselves and their abundance is dependent on yet other TFs. Much of the cellular differentiation to have different tissues and the dynamic molecular responses to stimuli are controlled transcriptionally. The identification of the exact oligonucleotides to which TF may be binding are described statistically by an observed enrichment of motifs of such TF binding sites by software like pscan. This tool further constraints the search with data from ChIP-Seq experiments from which the regions of DNA that is covered by a TF may be described.