ErillLab's repositories
LPEG_phages
Code and data for the analysis of TF-binding sites positional entropy in phage genomes, used in Mascolo et al. (2022)
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.
oprn_consv_calc
Aims to determine the structural conservation (i.e. gene order) of an operon within a given taxonomic clade.
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.
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
fast_PSSM_search
Lookahead implementation of biopython's motif search function
motif_merge
A set of functions to merge DNA sequence motifs
PhageReg_CompGen
Comparative genomics-based discovery of phage regulatory regions