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    70 repositories

    • Info-Theo-of-Composite-Motifs

      Public
      Computational simulations in support of our theoretical work on the information theory of composite motifs
      information-theorymolecular-evolutiontranscriptional-regulation
      Python
      •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

    • Markov_DNA_gen

      Public
      A Markov Model DNA sequence generator to generate pseudo-replicate sequences based on an input sequence
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 24, 2024Sep 24, 2024

    • FLEMINGO

      Public
      A project to generate models of regulated bacterial promoters using genetic programming
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 18, 2024Sep 18, 2024

    • QD-motifs

      Public
      Evolving TF-binding motifs using quality-diversity algorithms
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • fast_PSSM_search

      Public
      Lookahead implementation of biopython's motif search function
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • .github

      Public
      Profile repository of the ErillLab organization
      0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • CAG-MD

      Public
      Comparative genomics-assisted motif discovery
      Python
      •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • cgb3EM

      Public
      EM framework for CGB3
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 13, 2024Jun 13, 2024

    • PhageReg_CompGen

      Public
      Comparative genomics-based discovery of phage regulatory regions
      GNU General Public License v3.0
      •0•0•0•0•Updated May 30, 2024May 30, 2024

    • SPA

      Public
      Code and data used to perform the tAI analysis in deCarvalho et al. (2023)
      bioinformaticsphages
      Scheme
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 28, 2024Apr 28, 2024

    • cgb3

      Public
      Comparative genomics of prokaryotic transcriptional regulatory networks
      Python
      •
      GNU General Public License v3.0
      •0•1•2•0•Updated Apr 18, 2024Apr 18, 2024

    • cgb

      Public
      comparative genomics of transcriptional regulation in Bacteria
      Python
      •2•2•5•2•Updated Jul 6, 2023Jul 6, 2023

    • tAI

      Public
      tRNA adaptation index
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 17, 2023Jun 17, 2023

    • PHageR

      Public
      Analysis of host transcriptional regulation on phage genome sequences
      Python
      •
      MIT License
      •0•0•0•0•Updated May 30, 2023May 30, 2023

    • frameshift_detector

      Public
      Python
      •0•0•0•0•Updated May 29, 2023May 29, 2023

    • SMD

      Public
      Systematic discovery of TF-binding motifs
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 1, 2023May 1, 2023

    • phylo_seq_gen

      Public
      Pulls sequences of a reference gene from a set of genomes. A MSA of these sequences can be used to construct a phylogeny.
      Python
      •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • oprn_consv_calc

      Public
      Aims to determine the structural conservation (i.e. gene order) of an operon within a given taxonomic clade.
      Python
      •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • ViPhy

      Public
      Virus Phylogeny System
      Python
      •0•1•0•0•Updated Mar 29, 2023Mar 29, 2023

    • LPEG_phages

      Public
      Code and data for the analysis of TF-binding sites positional entropy in phage genomes, used in Mascolo et al. (2022)
      bioinformaticsphagestranscriptional-regulations
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 26, 2023Feb 26, 2023

    • arg_gc

      Public
      Code for the analysis of the antimicrobial resistance gene (ARG) dissemination across the global plasmidome
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • SOS_Bacteroidetes

      Public
      Code for the analysis of the SOS network in the Bacteroidetes
      Python
      •0•0•0•0•Updated Jan 25, 2023Jan 25, 2023

    • pHunter

      Public
      Python second-order approximation to the PromoterHunter code
      bioinformaticspromoterstranscriptional-regulations
      Python
      •0•1•0•0•Updated Jan 24, 2023Jan 24, 2023

    • MD_GP

      Public
      A project to generate models of regulated bacterial promoters using genetic programming
      computational-biologygenetic-programming
      Python
      •1•0•0•1•Updated Jan 19, 2023Jan 19, 2023

    • SulfoTmp_Resist

      Public
      Code for the analysis of the origin of MGE-encoded sul/dfr
      Python
      •0•0•0•0•Updated Sep 13, 2022Sep 13, 2022

    • PHunt

      Public
      Python first-order approximation to the PromoterHunter code
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 2, 2022Jul 2, 2022

    • motif_merge

      Public
      A set of functions to merge DNA sequence motifs
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 8, 2022Jun 8, 2022

    • preMGE_TF

      Public
      Scanning MGE sequences for TF-binding motifs
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 9, 2022Jan 9, 2022

    • SOS_non_culturable_bacteria

      Public
      Using metagenomic data to characterize the SOS transcriptional response
      Python
      •0•0•0•0•Updated Nov 11, 2021Nov 11, 2021

    • blast_seq_filter

      Public
      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.
      Python
      •1•0•0•0•Updated Oct 6, 2021Oct 6, 2021