DOI: 10.6084/m9.figshare.30188251
title: RAZOR Database: PCR Primers and Gel Electrophoresis Images

description: <b>Overview </b>Zipped contents for the RAZOR database. RAZOR is a catalog of predicted and experimentally-validated PCR and qPCR primers designed against 20 different respiratory viruses and was created at the Janga Lab at Indiana University Indianapolis. <b>Contents</b>The zip file contains: <b>primers.tsv (file) </b>| a delimited file of all RAZOR primers, including viral targets, genomic coordinates, sequences, and physiochemical metadata. Explanations for each column are provided in the Column Descriptions section below. <b>razor_primers_filtered_pair_penalty_0.5.csv (file) </b>| a subset of primers.tsv; filtered to include only primer pairs whose Primer3 pair penalty score is less than 0.5. Represents an optimal set of PCR primers. <b>validated_primer_images (folder) </b>| a folder of 8 gel electrophoresis images. Shows results for 4 SARS-CoV-2 PCR primers and 4 SARS-CoV-2 qPCR primers. <b>Column Descriptions</b><b>id | </b>the unique id of the PCR primer pair <b>accession | </b>NCBI accession code for the target virus<b>virus_genome_abbreviated_name | </b>short unique identifier for the virus name<b>virus_genome_full_name | </b>complete name of the virus<b>virus_genome_isolate | </b>isolate of the virus <b>genome_length | </b>length of the virus genome (nt)<b>product_start | </b>genomic start coordinate of the PCR product (amplicon)<b>product_end | </b>end coordinate of the PCR product <b>product_size | </b>length of the PCR product (nt)<b>product_melting_temp | </b>melting temperature of the PCR product (°C)<b>primer_pair_self_complementarity_anywhere | </b>Tendency of forward and reverse PCR primers to bind to each other at any position in the primer sequences<b>primer_pair_self_complementarity_3' | </b>Tendency of forward primer to bind reverse in its 3' region<b>annealing_temp | </b>temperature at which both primers bind to the template sequence (°C)<b>primer_pair_tm_difference | </b>difference in forward and reverse primer melting temperatures (°C)<b>primer_pair_penalty_score | </b>Primer3 weighted penalty score for forward - reverse primer pair<b>forward_primer_start | </b>start coordinate of the forward primer<b>forward_primer_end | </b>end coordinate of the forward primer<b>forward_primer_size | </b>length of the forward primer (nt)<b>forward_primer_seq | </b>sequence of the forward primer <b>forward_primer_melting_temp | </b>melting temperature of the forward primer (°C)<b>forward_primer_gc% | </b>Guanine (G) - Cytosine (C) content of the forward primer sequence (%)<b>forward_primer_self_complementarity_anywhere | </b>Tendency of the forward primer to self-bind anywhere<b>forward_primer_self_complementarity_3' | </b>Tendency of the forward primer to self-bind in its 3' region<b>forward_primer_hairpin_stability | </b>Penalty weight of the most stable expected forward primer hairpin structure<b>forward_primer_delta_g | </b>Gibbs free energy required to break the most stable expected forward primer hairpin structure (kJ/mol)<b>forward_primer_penalty_score | </b>Primer3 penalty score for the forward primer<b>reverse_primer_start | </b>start coordinate of the reverse primer<b>reverse_primer_end |</b><b> </b>end coordinate of the reverse primer <b>reverse_primer_size | </b>length of the reverse primer (nt)<b>reverse_primer_seq | </b>sequence of the reverse primer<b>reverse_primer_melting_temp | </b>melting temperature of the reverse primer (°C)<b>reverse_primer_gc% | </b>Guanine (G) - Cytosine (C) content of the reverse primer sequence (%)<b>reverse_primer_self_complementarity_anywhere | </b>Tendency of the reverse primer to self-bind anywhere<b>reverse_primer_self_complementarity_3' | </b>Tendency of the reverse primer to self-bind in its 3' region<b>reverse_primer_hairpin_stability | </b><b> </b>Penalty weight of the most stable expected reverse primer hairpin <b>reverse_primer_delta_g | </b>Gibbs free energy required to break the most stable expected reverse primer hairpin structure (kJ/mol)<b>reverse_primer_penalty_score | </b>Primer3 penalty score for the reverse primer<b>experimental_validation | </b>bool indicating whether or not the predicted primer pair has been experimentally validated<b>experimal_validation_image</b> | gel electrophoresis image or an equivalent demonstrating the experimental validation of the PCR primer pair <b>validation_group | </b>the organization credited for the validation experiment