CasPINS: An Integrated Web-Based Platform for CRISPR/TALEN gRNA Design, Primer Generation, and Indel Decomposition Analysis

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ID: 320153
2026
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Abstract
Abstract Genome editing researchers currently navigate multiple disconnected tools for guide RNA (gRNA) design, primer generation, and editing analysis—a fragmented workflow that introduces errors and limits reproducibility. CasPINS (Cas-Primer-Indel Suite) addresses this gap as an open-source, unified platform integrating the complete genome editing computational workflow into a single interactive web application accessible without programming expertise. The platform supports 90+ species, 14 CRISPR-Cas variants, TALEN design, and six editing modes. Primer design integrates with Ensembl and NCBI databases relative to cut sites, while indel quantification utilizes Non-Negative Least Squares (NNLS) decomposition of Sanger chromatograms with maximum signal extraction and R2-corrected conservative modes. Benchmarking demonstrates strong concordance with established tools, including a 68.8% recovery of CHOPCHOP gRNAs and 67.2% of CRISPOR gRNAs across five human benchmark genes, alongside an algorithmic agreement within 2.6 percentage points on gold-standard TIDE data. Ultimately, a step-count analysis shows that CasPINS significantly streamlines usability, reducing discrete user actions from 25 to 8 steps compared to the traditional sequential-tool pipeline.
Reference Key
openalex_W7167605928 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Rinki Dasgupta, Kaushik Das
Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag189
URL
https://doi.org/10.1093/bioadv/vbag189
Keywords Keywords not found

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