title: mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.
abstract: Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.
authors.affiliation: Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691, USA. yilmaz@cae.wisc.edu
authors.forename: L Safak
authors.initials: LS
authors.lastname: Yilmaz
authors.forename: Shreyas
authors.initials: S
authors.lastname: Parnerkar
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Noguera
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020407:Internet; D008962:Models, Theoretical; D015345:Oligonucleotide Probes / Q000032:analysis / Q000235:genetics*; D012313:RNA / Q000235:genetics; D012984:Software; D013816:Thermodynamics
chemical_list: D015345:Oligonucleotide Probes; D012313:RNA