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ames-rem2's Introduction

Ancestral (Sequence Reconstruction), Molecular Evolution, and Structure

Input

We use the data/mammalian_REM2_codons.SA.fasta.SLAC.json file as input, it is borrowed from the AOC-REM2 analysis.

This file is parsed using the scripts/ancestralevolution.py script. Resulting in data/REM2_AA.fasta, data/REM2_DNA.fasta', and data/REM2_MSA.fasta'

We calculate TN93 genetic distances on the `data/REM2_MSA.fasta' file

A bash command is used to split the multifasta file data/REM2_DNA.fasta' into single sequence fasta files in data /slac_asr`

We then generated PDB structures of all sequences using Colabfold's batch mode.

We extracted the Rank 1 PDB structure for each sequence

And calculated TM-Scores

Results are examined using the scripts in the notebooks folder

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