I have been given an unknown nucleotide sequence and need to analyze it using bioinformatic methods. I have already tried using getORF to look at the proteins but am not quite sure on what to do after that. I know that it is an archaea, but I was wondering if anyone can point me in the right direction of what to do.
Do you want to find out what these reads represent first (source genome(s))? The
Metagenomic Analysis > Kraken classification tools could be a start.
From there, what tools/workflows to use depend on your larger goals. The Galaxy Training Network tutorials cover many common bioinformatics analysis methods:
Thank you for your reply. I need to be able to suggest what the organism is, what it is related to, what genes does it have , how are they organised, structure.