Package: fealden
fealdenIntroductionFealdenis a command line tool to generate optimized structure switching DNA biosensors for fluorescent or electrochemical detection of trace amounts of a large number of biomolecule targets.  An abbreviatedbibliographyof works utilizing such nucleic acid-based biosensors is available below.Quick use with dockerFealden, with all binary dependencies enabled, can conveniently be run as a docker container:docker run --rm -it ghcr.io/paradoxdruid/fealden:latestDependenciesFealdenis written forPython 3.9+, and depends upon external secondary structure prediction routines.It can use either the excellentRNAstructure packagefrom the Mathews Lab, orUNAfold v3.8 and mfold v3.6by Markham and Zuker.Dependency Installation TipsRNAstructureavailable from the Mathews lab athttps://rna.urmc.rochester.edu/RNAstructure.htmlfealden requires the "text" interface version, for your operating systemhas a python_interface available, but requires C++ compilation stepRNAstructure version 6.4 needs corrections inrna_sources.hin thepython_interfacefolder:all references toTurboFolddirectory need to be replaced withsrcdirectorycan use commandsed -i 's/TurboFold\/src\//g' rna_sources.hto correctrequires installation ofswigsuch aspip install swigorconda install swigonceswiginstalled andrna_sources.hcorrected, enter thepython_interfacedirectory and run:make swigmake interface-from-distutilsupdate.envfile (see below) with path to RNAstructureUNAfold and mfoldversion 3.8 of UNAfold is available from sourceforge:https://rnaspace.sourceforge.net/software/unafold-3.8.tar.gzonce unzipped, enter theunafold-3.8directory and run:./configure --prefix=/A/GOOD/PATH/FOR/USER(for instance,/home/user/unafold-final)makemake installupdate.envfile (see below) with path toHYBRID_SS_MINin UnafoldYou will also need the programsir_graphincluded in version 3.6 of mfold, available athttp://www.unafold.org/download/mfold-3.6.tar.gzonce unzipped, enter themfold-3.6directory and run:./configure --prefix=/A/GOOD/PATH/FOR/USER(for instance,/home/user/mfold-final)makemake installupdate.envfile (see below) with path toSIR_GRAPHin UnafoldBefore use, you will need to create a.envfile following the format instructure.py.Example .env fileFEALDEN_BACKEND=mfold   # either 'mfold' or 'rnastructure'
HYBRID_SS_MIN=/home/username/unafold-new/bin/hybrid-ss-min
SIR_GRAPH=/home/username/mfold/bin/sir_graph
RNASTRUCTURE=/home/username/RNAstructureUsageTo useFealden:python -m fealden "TATATAA" 1(Where"TATATAA"is the input binding/recognition element (such as an aptamer), and1indicates whether the binding element is predominantly double-stranded (0) or single-stranded (1) in the binding-active state.)Fealdengenerates a .csv file of optimized biosensor sequences along with scoring metrics.ContributorsFealdenis developed as academic software by theBonham Laband Dr. Andrew J. Bonham at theMetropolitan State University of Denver.  It is licensed under the GPL v3.0.Contributors include: Dr. Andrew J. Bonham /@Paradoxdruid(initial and ongoing development), Jody Stephens /@23jodys(early implementation), Becky Addison (early implementation), Aviva Bulow /@aviva-bulow(code rewrite and development of current approach), and Austin Haider /@WallFacerGibbs(further development).BibliographyTranscription Factor Beacons for the Quantitative Detection of DNA Binding ActivityQuantification of Transcription Factor Binding in Cell Extracts Using an Electrochemical, Structure-Switching BiosensorElectrochemical Aptamer Scaffold Biosensors for Detection of Botulism and Ricin ProteinsStructure-switching biosensors: inspired by Nature