ErillLab/cgb

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Python
Created almost 9 years ago
Updated over 1 year ago

ErillLab/cgb

ErillLab

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comparative genomics of transcriptional regulation in Bacteria

collectf

CollecTF database implementation

gpu_pssm

A GPU-based implementation of sliding window PSSM scoring.

Markov_DNA_gen

A Markov Model DNA sequence generator to generate pseudo-replicate sequences based on an input sequence

tAI

tRNA adaptation index

FLEMINGO

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

ViPhy

Virus Phylogeny System

SPA

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

vibrio-biofilm-formation

In silico analysis of promoter architecture for biofilm formation genes involved in Vibrio cholerae

pHunter

Python second-order approximation to the PromoterHunter code

control_seq_gen

Generates control sequences for motif analysis. Goal is to maintain the statistical parameters of the input sequences (i.e. nucleotide composition) without recapitulating the sites of interest.

LPEG_phages

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