hybseek: Pathogen primer design tool for diagnostic multi-analyte assays
Computer Methods and Programs in Biomedicine
An efficient algorithm for finding gene-specific probes for DNA microarrays
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
An incremental algorithm for efficient unique signature discoveries on DNA databases
Proceedings of the 2010 ACM Symposium on Applied Computing
Distributed stream processing with DUP
NPC'10 Proceedings of the 2010 IFIP international conference on Network and parallel computing
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Motivation: 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. Availability: Freely available (LGLP) along with source code and additional documentation at http://pathport.vbi.vt.edu/YODA Contact: enordber@vbi.vt.edu