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Table 3 Species nomenclature used in biochemical models

From: Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy

Species Label

Species

Rpoly

RNA polymerase

closed_Rpoly_prom_ns*

RNA polymerase in a closed-complex with the average genomic mRNA operon promoter

closed_Rpoly_prom_s*

RNA polymerase in a closed-complex with the average genomic sRNA operon promoter

closed_Rpoly_prom_reporter

RNA polymerase in a closed-complex with the reporter mRNA promoter on the plasmid

open_Rpoly_prom_ns*

RNA polymerase in an open-complex with the average genomic mRNA operon promoter

open_Rpoly_prom_s*

RNA polymerase in an open-complex with the average genomic sRNA operon promoter

open_Rpoly_prom_reporter

RNA polymerase in an open-complex with the reporter mRNA promoter on the plasmid

Rpoly_operon_ns*

RNA polymerase elongating the average genomic mRNA transcript from the average genomic mRNA operon

Rpoly_operon_s*

RNA polymerase elongating the average genomic sRNA transcript from the average genomic sRNA operon

Rpoly_reporter

RNA polymerase elongating the reporter mRNA transcript from the plasmid

incom_mRNA*

Nascent average genomic mRNA

incom_mRNA_small*

Nascent genomic mRNA where its final length is approximately 90% of the average genomic mRNA

incom_mRNA_reporter

Nascent reporter mRNA

mRNA*

Average genomic mRNA (represented as the length of the average genomic mRNA gene)

mRNA_small*

Genomic mRNA that is approximately 90% of the average genomic mRNA

stable_RNA*

Average genomic sRNA (represented as the length of the average genomic sRNA operon)

mRNA_reporter

Reporter mRNA – the mRNA of interest

operon_ns*

Average genomic mRNA operon

operon_s*

Average genomic sRNA operon

plas

Reporter promoter on the plasmid

v

Cell volume

*

Refers to species used exclusively in the gene expression model that incorporates the host's genome

  1. List of species names used in the two versions of the model.
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BMC Bioinformatics

ISSN: 1471-2105

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