GeneSearch shRNA: Intro

GeneSearch shRNA (GS2) is a search engine that returns shRNA and ORF downloadable CSV data, courtesy of The Broad Institute, that are relevant to the Genes Symbols, IDs, and Transcript ID’s searched, with the ability to handle a variety of multiple inputs of each type, along with detailed links to the Genetic Perturbation Platform (GPP) web portal and NCBI. (Prototype on my GitHub) 

The search engine uses publicly available resources from the GPP web portal, built with scala js and bootstrap CSS for added functionality and usability for genetic researchers.

The Broad Institute’s GPP web portal is a research tool for scientists to plan and choose the best model system and experimental readouts in functional investigations of mammalian genomes that can reveal how genetic alterations lead to changes in phenotype. (Used for Gene editing in experiments to research gene expression/suppression and its effect on diseases to develop gene therapy)

Technologies in the web portal include libraries of short hairpin RNAs (shRNAs), CRISPR/Cas9 constructs, and open reading frames (ORFs) to knockdown or over-express genes, in addition to other techniques such as TALEN and CRISPR for genome editing and “tough decoy”, constructs to inhibit microRNAs.

GS2 validates inputs through NCBI, handles both mouse and human gene symbols, ids, and transcripts, checks if genes symbols go by alternative names, handles multiple inputs/lack of gene symbol capitalization, has a single input field, and requires less clicking than the current GPP’s “Search by Gene” web page.

Since building this prototype in Nov 2019, I noticed the GPP had made additional updates to other parts of their web portal, my favorite being their CRISPick software tool for CRISPR gene editing.

CRISPick ranks and picks candidate CRISPRko/a/i sgRNA sequences to maximize on-target activity for targets (genes to be edited/suppressed/expressed), with the ability to choose your Reference genome, your CRISPR mechanism, and enzyme to find the optimal sgRNA for your gene editing experiments! 

A very cool tool that is used for developing gene therapies of the future!!

- Dom

May 26, 2021, 11:27 p.m.