title: YODA: selecting signature oligonucleotides.
abstract: BACKGROUND
  Selecting oligonucleotide probes for use in microarray design, and other applications requiring signature sequences, involves identifying sequences which will bind strongly to their intended target, while binding only weakly (or preferably, not at all) to non-target sequences which may be present in the hybridization reaction. While many tools to assist in selection of such sequences exist, all the ones we examined lack important oligo design and software features.
  
  
  RESULTS
  YODA is an application for assisting biological researchers in selecting signature sequences. It incorporates a custom sequence similarity search to find potential cross-hybridizing non-target sequences. For this task, most oligo design tools rely on BLAST, which is ill suited for it due to an unacceptable risk of false negatives. YODA supports multiple probe design goals including single-genome, multiple-genome, pathogen-host and species/strain-identification. A graphical interface is provided as well as a command-line interface, both of which support many user-controlled parameters. YODA is easy to install and use and runs on Windows, Mac OS X and Linux platforms.
  
  
  BACKGROUND
  Freely available (LGLP) along with source code and additional documentation at http://pathport.vbi.vt.edu/YODA CONTACT: enordber@vbi.vt.edu.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. enordber@vbi.vt.edu
authors.forename: Eric K
authors.initials: EK
authors.lastname: Nordberg
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D015345:Oligonucleotide Probes