Package: oligo-melting
oligo-meltingA Python3 package for melting temperature calculation of oligonucleotides hybridization and secondary structures.FeaturesHandles DNA:DNA, RNA:RNA and DNA/RNA hybridizations.Corrects for both salt and chemicals.Compatible with UNAfold (OligoArrayAux) output for direct salt and chemicals (denaturants) correction.Produces melting curves for the provided sequence.Input either as single sequence or FASTA file.Slightly faster than BioPython.SeqUtils.MeltingTemp.Provides dG, dS and dH alongside melting temperature.LimitationsDoes not handle mismatches or dangling endsDoes not handle ambiguous basesInstallationToinstall, run the following:git clone http://github.com/ggirelli/oligo-melting
cd oligo-melting
sudo -H pip3 install .Touninstallrun the following from within the repository folder:sudo -H pip3 uninstall oligo_meltingToupdate, first uninstall, and then run the following from within the repository folder.git pull
sudo -H pip3 uninstall oligo_melting
sudo -H pip3 install .UsageFrom command lineDuplexesThemelt_duplexcommand allows to calculate the melting temperature of a nucleic acid duplex, provided the sequence of one of the two strands.The hybridization delta free energy calculation is based on the N-N thermodynamic values in literature and is available for DNA:DNA[3], RNA:RNA[1] and DNA:RNA[2] duplexes. The melting temperature calculation is based on Santalucia, 1998[4]. Sodium and cagnesium concentration correction is based on the work of Owczarzy et al[5][6]. Formamide correction can be performed based on two different published models[7][8].Use the-toption to specify thetype of nucleic acid duplex.Use--fa-modeto switch between linear melting temperatureformamide-based correction[7] and linear ΔG formamide-based correction[8].Use--fa-mvaluetogether with--fa-mode wrightto specify them-valuefor the formamide-based correction.Provide the path to afasta fileinstead of a single sequence to calculate the melting temperature of every sequence in the file.Use the-voption to trigger the verbose mode, which provides moredetailsfor every single sequence.Use-Cfor the temperature indegree Celsiusinstead of Kelvin.Use--out-curveto specify a file where to save estimated single-sequencemelting curveswith temperature range and step around the melting temperature as defined with--t-curve.Secondary structureThemelt_secstrscript allows to correct the melting temperature of a nucleic acid secondary structure, previously calculated with OligoArrayAux, and to produce the corresponding melting curves.As a libraryImport the package and use the corresponding functions.importoligo_meltingasOligoMeltseq="CAGTCAGTCGATC"# Calculate melting temperature for 25uM oligos(name,g,h,s,tm,seq)=OligoMelt.Duplex.calc_tm(seq,oligo_conc=25e-6)print(tm)# Adjust for 300 mM [Na+]tm=OligoMelt.Duplex.adj_ions(tm,0.3,0,seq)print(tm)TheDuplexmodule contains functions for duplex hybridization and melting temperature calculation, while theSecStrmodule contains similar methods for evaluating secundary structure melting temperatures.References[1]: Freier et al, PNAS(83), 1986;[2]: Sugimoto et al, Biochemistry(34), 1995.[3]: Allawi & Santalucia, Biochemistry(36), 1997;[4]: SantaLucia, PNAS(95), 1998;[5]: Owczarzy et al, Biochemistry(43), 2004;[6]: Owczarzy et al, Biochemistry(47), 2008;[7]: McConaughy et al, Biochemistry(8), 1969;[8]: Wright et al, Appl. env. microbiol.(80), 2014.LicenseMIT License
Copyright (c) 2017 Gabriele GirelliThis project comes from thepotpourrisandbox.  \( ﾟヮﾟ)/