OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.

ABSTRACT: Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the spe

SUBMITTER: Beliveau BJ 

PROVIDER: S-EPMC5877937 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature