ErillLab

cgb

comparative genomics of transcriptional regulation in Bacteria

FLEMINGO

A project to generate models of regulated bacterial promoters using genetic programming

LPEG_phages

Code and data for the analysis of TF-binding sites positional entropy in phage genomes, used in Mascolo et al. (2022)

SPA

Code and data used to perform the tAI analysis in deCarvalho et al. (2023)

tAI

tRNA adaptation index

ViPhy

Virus Phylogeny System

blast_seq_filter

A versatile script for pulling BLAST results. Specifically intended to be used to pull promoter sequences of a set of proteins and filter those promoter sequences based off a set similarity threshold.

frameshift_detector

oprn_consv_calc

Aims to determine the structural conservation (i.e. gene order) of an operon within a given taxonomic clade.

PHageR

Analysis of host transcriptional regulation on phage genome sequences

phylo_seq_gen

Pulls sequences of a reference gene from a set of genomes. A MSA of these sequences can be used to construct a phylogeny.

soa

A pipeline for systematic operon analysis (soa) in aims to elucidate genome wide transcription regulatory networks.

.github

Profile repository of the ErillLab organization

arg_gc

Code for the analysis of the antimicrobial resistance gene (ARG) dissemination across the global plasmidome

CAG-MD

Comparative genomics-assisted motif discovery

cgb3

Comparative genomics of prokaryotic transcriptional regulatory networks

cgb3EM

EM framework for CGB3

fast_PSSM_search

Lookahead implementation of biopython's motif search function

MD_GP

A project to generate models of regulated bacterial promoters using genetic programming

motif_merge

A set of functions to merge DNA sequence motifs

PhageReg_CompGen

Comparative genomics-based discovery of phage regulatory regions

PHunt

Python first-order approximation to the PromoterHunter code

pHunter

Python second-order approximation to the PromoterHunter code

preMGE_TF

Scanning MGE sequences for TF-binding motifs

QD-motifs

Evolving TF-binding motifs using quality-diversity algorithms

SMD

Systematic discovery of TF-binding motifs

SOS_Bacteroidetes

Code for the analysis of the SOS network in the Bacteroidetes

SOS_non_culturable_bacteria

Using metagenomic data to characterize the SOS transcriptional response

SulfoTmp_Resist

Code for the analysis of the origin of MGE-encoded sul/dfr

TF_GP

A project to generate models of regulated bacterial promoters using genetic programming