What question did this study set out to answer?

The goal is to create a unified platform for genome editing to enhance design accuracy and usability.

July 9, 2026Bioinformatics Advances0 citationsOpen Access

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

RDRinki DasguptaThe University of Texas at Austin KDKaushik DasNational Institute of Technology Jamshedpur

Key Points

The goal is to create a unified platform for genome editing to enhance design accuracy and usability.
Developed an open-source platform integrating gRNA design, primer generation, and editing analysis tools.
Supported over 90 species and various CRISPR-Cas variants with TALEN design capabilities.
Utilized Non-Negative Least Squares (NNLS) for indel quantification with Sanger chromatograms.
Achieved a recovery rate of 68.8% for CHOPCHOP gRNAs and 67.2% for CRISPOR gRNAs across five benchmark genes.
Demonstrated algorithmic agreement within 2.6 percentage points of gold-standard data from TIDE.
Reduced the number of user steps from 25 to 8 compared to traditional workflows.

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.

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Cite This Study

Dasgupta et al. (Tue,) studied this question.

synapsesocial.com/papers/6a4f3b382b81a944af5752bd https://doi.org/https://doi.org/10.1093/bioadv/vbag189

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