REHUNT: a reliable and open source package for restriction enzyme hunting

BACKGROUND: Restriction enzymes are used frequently in biotechnology. However, manual mining of restriction enzymes is challenging. Furthermore, integrating available restriction enzymes into different bioinformatics systems is necessary for many biotechnological applications, such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Thus, in the present study, we developed the package REHUNT (Restriction Enzymes HUNTing), which mines restriction enzymes from the public database REBASE using a series of search operations. RESULTS: REHUNT is a reliable and open source package implemented in JAVA. It provides useful methods and manipulations for biological sequence analysis centered around restriction enzymes contained in REBASE. All available restriction enzymes for the imported biological sequences can be identified by REHUNT. Different genotypes can be identified using PCR-RFLP based on REHUNT for single nucleotide polymorphism (SNP), mutations, and the other variations. REHUNT robustly recognizes multiple inputs with different formats, e.g. regular DNA sequences, variation-in-sequence indicated by IUPAC code, as well as variation-in-sequence indicated by dNTPs format. Variations including di-, tri-, and tetra-allelic types and indel formats are also acceptable. Furthermore, REHUNT provides classified restriction enzymes output, including IUPAC and general sequence types, as well as commercial and non-commercial availabilities. REHUNT also enables analysis for high throughput screening (HTS) technologies. CONCLUSIONS: REHUNT is open source software with GPL v3 license and can be run on all platforms. Its features include: 1) Quick restriction enzymes search throughout a sequence based on the Boyer-Moore algorithm; 2) all available restriction enzymes provided and regularly updated from REBASE; 3) an open source API available of integrating all types of bioinformatics systems and applications; 4) SNP genotyping available for plant and animal marker-assisted breeding, and for human genetics; and 5) high throughput analysis available for Next Generation Sequencing (NGS). REHUNT not only to effectively looks for restriction enzymes in a sequence, but also available for SNP genotyping. Furthermore, it can be integrated into other biological and medical applications. REHUNT offers a convenient and flexible package for powerful restriction enzymes analyses in association studies, and supports high throughput analysis. The source codes and complete API documents are available at SourceForge: https://sourceforge.net/projects/rehunt/, GitHub: https://github.com/yuhuei/rehunt, and at: https://sites.google.com/site/yhcheng1981/rehunt.