This code finds identical continuous segments between two proteins. It is here used to compare SARS-CoV-2 and human proteins.
The main script is findallsegments.py. It reads the viral and human sequences from directory sequences and writes
the identical segments found for each viral protein in directory rawsegments.
Function findsegments in findallsegments.py is where the systematic window sliding search is done.
The two remaining scripts, sortsegments.py and extractproteins.py, are mostly about organizing the results for better readability.
Script sortsegments.py sorts the segments obtained by length and occurrence and writes the result to file sortedsegments.txt.
The script extractproteins.py rewrites the results to file proteinmatches.txt in a protein-centric fashion rather that segment-centric.
This last script accepts an optional list of proteins. If a list is provided, proteins that are not in the list are excluded from
resulting matches.
Human sequences file sequences/human_reviewed_canon.fasta was downloaded from UniProt on June 3, 2020
using the following query: organism:"Homo sapiens (Human) [9606]" AND reviewed:yes.
SARS-Cov-2 viral sequences files sequences/r1ab_sars2.fasta, sequences/spike_sars2.fasta, etc,
were downloaded from UniProt on June 3, 2020 using the following query: organism:sars-cov-2 AND reviewed:yes.
The sequence of viral orf10 (UniProt A0A663DJA2, NCBI YP_009725255.1) was downloaded separately from UniProt, also on June 3, 2020.