KASP-Hedgehog: Efficient and routine tool for allele specific primer design using multidisciplinary data types.

Abstract

The Integration of known nucleotide variations in breeding programs and medical assessments demands the ability to scan and validate thousands of gene-affected SNPs. Designing PCR primers targeting these SNPs require computational tools could generate accurate and target-specific primers using multidisciplinary data types with high accuracy. KASP-Hedgehog is a local-installation, simple and routine tool for allele-specific PCR primer design. KASP-Hedgehog gives user the ability to design KASP primer from a variety of genomic data, extract bi-allelic SNPs for genomic sequences with unknown nucleotide variations and select SNPs with potential effect depending on gene annotation. This tool can use user-provided or self-produced SNPs database to create allele-specific primers with degenerate structure in order to enhance PCR assay selectivity and increase amplification reaction. Additionally, it run an in silico PCR test for designed primers against provided FASTA sequences in order to increase primers selectivity and provide user more information. Moreover, it has interactive and user-friendly graphical user interface (GUI) in addition to a command-line package could be integrated in different bioinformatics pipelines.