I hope everyone is doing well! I was wondering if someone could please help me in that I want to discover Lineage-Specific proteins in a genus of archaea using Orthofinder. Therefore, could someone please help me either with what file from the Orthofinder output to use or if there are any scripts (python/bash) to collect this data.
In other words, I want to find the proteins that are only found within a specific genus of archaea; therefore, could someone please help me find this information please and thank you.
Calvin Cornell you can use OrthoFinder to identify lineage-specific proteins within a specific genus of archaea. Here are the steps to do so:
To identify lineage-specific proteins for your specific genus of archaea:
Here's a simplified example of how you might approach this using Python and the presence/absence matrix:
pythonCopy code# Load the presence/absence matrix (tab-delimited file) # Rows are genes, columns are species/strains # 1 indicates presence, 0 indicates absence # Filter genes from your genus genus_genes = presence_absence_matrix[genus_index] # Check if a gene is present only in your genus lineage_specific_genes = [] for gene_id, presence_vector in enumerate(genus_genes): if sum(presence_vector) == 1: # Gene is present only in one species lineage_specific_genes.append(gene_id) # Retrieve the protein sequences of lineage-specific genes lineage_specific_proteins = [] for gene_id in lineage_specific_genes: protein_sequence = retrieve_protein_sequence(gene_id) # Implement this function based on your dataset lineage_specific_proteins.append(protein_sequence) # Save or analyze the lineage-specific protein sequences
Please adapt this code to your specific dataset and programming environment. The key is to filter orthogroups and genes based on your genus of interest and identify those that are unique to your genus. Then, retrieve the protein sequences associated with those genes.
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