Analysis of Orthologous Collections (AOC) on REM2, REM2: a member of the RGK (Rem, Rem2, Rad, and Gem/Kir) family of small GTPases.
This repository contains all code, data, and results for the evolutionary analysis of mammalian REM2.
git clone https://github.com/aglucaci/AOC-REM2.git
cd AOC-REM2
conda env create -f environment.yml
This creates the 'AOC_REM2' environment which you will need to enable by running : conda activate AOC_REM2
Set your cluster configurations in the cluster.json file. If needed, contact your system administrator for guidance on how to configure your queue and processors per node.
The data folder contains data from NCBI. Specifically, the structure is as follows:
── data/mammalian_REM2
│ ├── Rem2_orthologs.csv
│ ├── Rem2_refseq_protein.fasta
│ ├── Rem2_refseq_transcript.fasta
When ready to use the Snakemake pipeline type, from the working directory:
bash run_HPC_AOC.sh
This will run all of the analysis code.
The results of our analyses are populated in the results/mammalian_REM2 folder.
This folder will contain all intermediate files from all steps of the workflow, and the products of selection analyses as JSON-files.
This folder scripts holds a number of useful scripts used for our analyses. You do not need to interact with or call these scripts individually, instead they are used as part of the workflow.
Run these notebooks independently after the selection analyses have finished.
executiveSummary.ipynb this notebook creates a high-level overview of the selection analysis results.
SummarizeBUSTED_ModelTest.ipynb summaries the results from the BUSTED-family of analyses and outputs the table: mammalian_REM2_BUSTED_ModelTest.csv in the tables folder
SummarizeFEL-FDR.ipynb summaries the results from the FEL analysis, and outputs the following table: mammalian_REM2_FEL_Results_FDR_adjusted_mapped.csv, also performs multiple test correction (FDR) and maps alignment sites the Human reference sequence.
SummarizeMEME-FDR.ipynb summaries the results from the MEME analysis, and outputs the following table: mammalian_REM2_MEME_Results_FDR_adjusted_mapped.csv, also performs multiple test correction (FDR) and maps alignment sites the Human reference sequence.
SummarizeBGM.ipynb summarizes results from the BGM analysis. It creates visualizations and outputs a table to tables, mammalian_REM2_BGM_Results_Mapped.csv
AlignmentMapper.ipynb creates a mapping between the Human sites in the alignment (ungapped) and the gapped alignment. This is output to the results folder as mammalian_REM2_codons.SA.FilterOutliers.fasta_AlignmentMap.csv`
AlignmentProfiler.ipynb creates a number of useful figures and calculates descriptive statistics for a multiple sequence alignment.
ViewNewick.ipynb A useful notebook for examining Newick trees, and creating a visualization-friendly version of the Newick file, by shortening labels of nodes.
View_TN93_GeneticDistances.ipynb A useful notebook for examining TN93 genetic distances. Creates a histogram of the pair-wise distances.
Model_Structure.ipynb is used to map sites from MEME and FEL analyses to the Human references and creates an output table used for visualization in tables, mammalian_REM2_StructureView.csv. This is used for the ObservableHQ interactive notebook. https://observablehq.com/@aglucaci/structure-rem2.