Conducts regressions on the cleavage efficiencies of single guide RNAs (sgRNAs). TSAM is a two-step averaging method that first predicts cleavage efficiency scores using an XGBoost regressor, and then constructs a support vector machine (SVM) regression model using the pHMM features combined with the top-ranked features selected by the first step. It was tested on eleven benchmark datasets containing thousands of sgRNAs editing human, mouse and zebrafish genome sequences and on additional twelve datasets of different expression system.
Permits to conduct analysis of datasets associated with custom nuclease applications. GUIDEseq provides a flexible platform with more than 60 adjustable parameters allowing the user to customize sequence aggregation criteria. It returns an off-target cleavage prediction score for each site based on the complementarity to the input target sequence. The tool uses activity models generated from a variety of experimental datasets.
Identifies, quantifies and visualizes genuine genome editing events form CRIPR amplicon sequencing data. ampliCan can determine the true mutation frequencies of CRISPR experiments from high-throughput DNA amplicon sequencing. It allows scaling to genome-wide experiments and quantification for the heterogeneity of reads. This software executes the complete pipeline from alignment to interpretation and check for biases at all steps.
Analyses sequences and permits users to manage molecular biology data. MolQuest provides several programs for molecular biology data processing. It contains options for sequence editing, primer design, internet database searches, gene prediction, promoter identification, regulatory elements mapping, patterns discovery protein analysis, multiple sequence alignment, phylogenetic tree reconstruction, and a wide variety of other functions.
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