5. Glossary

NAME	DESCRIPTION
Azimuth	A machine learning based tool to predict the on-target binding potential associated with a specific sgRNA sequence1
Biophysical Model	The modeling of a biological process through the mathematical representation of physical properties of the system, including the thermodynamics of various molecular interactions and processes.
CRISPR-interference	The use of a catalytically-inactive Cas9 (dCas9) to interfere with the transcription of a target gene, decreasing expression rates.
Endogenous DNA	Chromosomal or plasmid DNA originating from the wild-type host.
Entropy (statistical)	Describes the distribution of likelihoods of a system being in a given state. A larger entropy indicates a more even distribution of the likelihood of being in each of the possible states of the system, or less predictable state in the system at a given time. Entropy is often associated with the disorder within a given system.
Entropy Score	sgRNAble employs the concept of statistical entropy in order to rank sgRNAs based on the likelihood of off-target binding. A lower Entropy Score indicates a less disordered system, in which there is a greater likelihood of Cas9 being bound to the intended target site, based on the binding probabilities predicted by the biophysical model and Cas9 binding mechanics.
Exogenous DNA	Chromosomal or plasmid DNA originating from outside of the wild-type host (ie. engineered plasmids).
Extra-Chromosomal DNA	DNA not encoded in the chromosome (ie. plasmid DNA / viral DNA)
FASTA Format	A common file format for the representation of nucleic acid and protein sequences.
Off-Target Effects	The binding of Cas9 to a DNA sequence other than the intended target site. The likelihood of off-target binding is influence by the sequence of the sgRNA and off-target site. This can lead to off-target DNA cleavage when using a wild-type Cas9 endonuclease.
Open Reading Frame	The sequence between two stop codons a specific reading frame. These regions often encode protein-coding genes. Prodigal predicts start codons, resulting sequences representing gene-coding sequences (CDSs).
Single Guide RNA (sgRNA)	An engineered guide RNA combining the two guide RNA transcripts that complex with Cas9, in order to direct Cas9 binding to its target sequence (crRNA / tracrRNA). This results in a single RNA transcript forming the complex with Cas9.

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