RAZOR Database: PCR Primers and Gel Electrophoresis Images

Overview 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. ContentsThe zip file contains: primers.tsv (file) | 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. razor_primers_filtered_pair_penalty_0.5.csv (file) | 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. validated_primer_images (folder) | a folder of 8 gel electrophoresis images. Shows results for 4 SARS-CoV-2 PCR primers and 4 SARS-CoV-2 qPCR primers. Column Descriptionsid | the unique id of the PCR primer pair accession | NCBI accession code for the target virusvirus_genome_abbreviated_name | short unique identifier for the virus namevirus_genome_full_name | complete name of the virusvirus_genome_isolate | isolate of the virus genome_length | length of the virus genome (nt)product_start | genomic start coordinate of the PCR product (amplicon)product_end | end coordinate of the PCR product product_size | length of the PCR product (nt)product_melting_temp | melting temperature of the PCR product (°C)primer_pair_self_complementarity_anywhere | Tendency of forward and reverse PCR primers to bind to each other at any position in the primer sequencesprimer_pair_self_complementarity_3' | Tendency of forward primer to bind reverse in its 3' regionannealing_temp | temperature at which both primers bind to the template sequence (°C)primer_pair_tm_difference | difference in forward and reverse primer melting temperatures (°C)primer_pair_penalty_score | Primer3 weighted penalty score for forward - reverse primer pairforward_primer_start | start coordinate of the forward primerforward_primer_end | end coordinate of the forward primerforward_primer_size | length of the forward primer (nt)forward_primer_seq | sequence of the forward primer forward_primer_melting_temp | melting temperature of the forward primer (°C)forward_primer_gc% | Guanine (G) - Cytosine (C) content of the forward primer sequence (%)forward_primer_self_complementarity_anywhere | Tendency of the forward primer to self-bind anywhereforward_primer_self_complementarity_3' | Tendency of the forward primer to self-bind in its 3' regionforward_primer_hairpin_stability | Penalty weight of the most stable expected forward primer hairpin structureforward_primer_delta_g | Gibbs free energy required to break the most stable expected forward primer hairpin structure (kJ/mol)forward_primer_penalty_score | Primer3 penalty score for the forward primerreverse_primer_start | start coordinate of the reverse primerreverse_primer_end | end coordinate of the reverse primer reverse_primer_size | length of the reverse primer (nt)reverse_primer_seq | sequence of the reverse primerreverse_primer_melting_temp | melting temperature of the reverse primer (°C)reverse_primer_gc% | Guanine (G) - Cytosine (C) content of the reverse primer sequence (%)reverse_primer_self_complementarity_anywhere | Tendency of the reverse primer to self-bind anywherereverse_primer_self_complementarity_3' | Tendency of the reverse primer to self-bind in its 3' regionreverse_primer_hairpin_stability | Penalty weight of the most stable expected reverse primer hairpin reverse_primer_delta_g | Gibbs free energy required to break the most stable expected reverse primer hairpin structure (kJ/mol)reverse_primer_penalty_score | Primer3 penalty score for the reverse primerexperimental_validation | bool indicating whether or not the predicted primer pair has been experimentally validatedexperimal_validation_image | gel electrophoresis image or an equivalent demonstrating the experimental validation of the PCR primer pair validation_group | the organization credited for the validation experiment