Hi all, I am a microbiology student with little knowledge to bioinformatics and programming outside of Illumina reads alignment and denovo assembly. Recently I was tasked to compare two closely related strains of the same species and to identify unique pathways amongst the two that allow each to specialize in their niche based on the complete sequences present on genbank prior to any wet lab procedures.
To approach this, I plan to extract all open reading frames from both strains, pull out shared/highly similar ORF and unique ORF, then find the pathway the unique ORFs are involved in to draw conclusion. I've extracted all open reading frames from both organisms using prodigal, based solely on the in frame non-interupted sequence between start and stop codon. Each of strain have about 2000 real and hypothetical AA sequences.
now I'm stuck trying to extract shared and unique sequences from both organisms. Are there any programs that is suitable for this task? All replies are appreciated!
To approach this, I plan to extract all open reading frames from both strains, pull out shared/highly similar ORF and unique ORF, then find the pathway the unique ORFs are involved in to draw conclusion. I've extracted all open reading frames from both organisms using prodigal, based solely on the in frame non-interupted sequence between start and stop codon. Each of strain have about 2000 real and hypothetical AA sequences.
now I'm stuck trying to extract shared and unique sequences from both organisms. Are there any programs that is suitable for this task? All replies are appreciated!
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