Blaster.rb

Ruby script for calling bacterial probes. Bacterial genome files cut up to 60mers, screened for suitability, and blasted with a local copy of NCBI Blast, results narrow down to lists of good candidates for each genome in the queue that are unique at the species or genus level.

Downloads

Download Blaster.rb package [zip]
Original package based on 40mers [zip] [github]

Contact

Richard W. Hyman » email

Manuscript Reference

Targeted and highly multiplexed detection of microorganisms employing an ensemble of molecular probes; Weihong Xu, Sujatha Krishnakumar, Molly Miranda, Michael A. Jensen, Marilyn Fukushima, Curtis Palm, Eula Fung, Ronald W. Davis, Robert P. St.Onge, and Richard W. Hyman; Applied and Environmental Microbiology, 2014; in press.

Also see Use of Molecular Probes with Barcodes to Identify Microbes

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