SeniorProject

Identification and Characterization of Butyrate-Producing Species in the Human Gut Microbiome

Introduction

In this project we explore genomes from HMP 1 to attempt to identify species that may be capable of butyrate production based on the presence of enzyme-encoding genes involved in the pathway(s) of butyrate production. In this repository, you will find the code and methods used for data formatting, protein alignments, and data analysis.

DATA:

Species = http://downloads.ihmpdcc.org/data/reference_genomes/body_sites/Gastrointestinal_tract.cds.fsa ("Gastrointestinal_tract.cds.fsa") Pathway Proteins = https://www.ncbi.nlm.nih.gov/nuccore/DQ987697.1?report=fasta** (Save as "butyrate_genes_BTC&BK.fasta"), https://www.ncbi.nlm.nih.gov/nuccore/AY796317.2?report=fasta** (Save as "butyryl_COA_transferase_BCT.fasta"), https://www.ncbi.nlm.nih.gov/protein/WP_003420701.1?report=fasta (Save as "phosphate_butyryltransferase_BK.fasta", https://www.ncbi.nlm.nih.gov/protein/WP_003722496.1?report=fasta (Save as "butyrate_kinase_BK.fasta")

** partial CDS that will be translated to protein sequence during formatting.

HOW TO USE:

Step 1 - Data formatting

1. Collect data from HMP
2. Collect data from NCBI
3. run DataFormatting.py --> Creates fasta files for all protein sequences and all species

Step 2 - Alignments

1. run RunAlignments.py --> Creates xml files for each alignment, csv files for unprocessed results, and csv files for scored results

Step 3 - Analyses

1. pull 16s rRNA data and taxon info from Silva Database (batch download)
2. run Analyze_Data.py --> Creates csv output files for labeling taxon info, for formating input ANOVA files, and a fasta file for running the multiple sequence alignment on Clustal Omega
3. Run ANOVA.R with the output files from step 2
4. Run Clustal Omega multiple sequence alignment with output files from step 2
5. Interpret results with output taxon files from step 2, from the phylogenetic analysis, and from the ANOVA.