operOn.and.On

Leanie Williams

2025 01-07

Introduction

• Can we determine bacterial operon structure using the GFF and genome information?
• Can operons be used as the features for transcriptomic experiments?
• How do we find promoters?
• What are the regulators?

Methods

Work in progress

1. Features in an operon must be co-oriented.
   • co oriented would mean that the features are on the same strand (+ or -)
2. Features must be found serially.
   • serially means that the number of bases between features should not exceed 500 bases (note we will examine the threshold of bases and how it impacts the output)

input: gff output : csv

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Testing:

input: RdKW20.annot.gff

• sequence-region 1 1830138
• species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=727

Results

GFF to Operons

We define functions for parsing the GFF, finding operons based on our rules (see Methods), and returning the results as a csv. The csv contains a header Feature, Locus_tag, Gene_type, Operon_ID, Operon_Start, Operon_End, Strand and each feature (defined as genes or pseudogenes) is specified within an operon.

The user can include a separation threshold (--sep_thresh) which will specify how many bases between features. This parameter has a range between 0 and 500 bases, and a default of 500. This parameter informs the results in the columns oriented and oriented_nearby. If a feature is located on the '+' strand (sense), they receive a 1 and the '-' strand (antisense) is 0. The results of oriented_nearby are TRUE if the features are both on the same strand and located within the defined separation threshold, defining the operon.

BED formatted operons

The user may return an optional [BED] formatted file (--bed). The user may return a bed file for intergenic regions using --inter.

To do:

• argument parser
• define feature name, BED attributes (chromosome, start, stop, name, score, strand, ID, feature type, description etc etc...)