Apologies for asking such a broad and somewhat obvious question to some, but I am wanting to annotate a new transcriptome across several databases (inc. NCBI, Swissprot, Uniprot, custom databases) from my standalone BlastX server set-up on a cluster.
Whilst I am comfortable blasting against 1 database using BlastX. How can I go about annotating an assembly via multiple databases and collating all the information and the best suited hits? Can this be run in one process or do I need specialised scripts to combine and sort out all the information collated?
Answer may be obvious to many, but I am still learning more on command line and scripting.
Thanks for the help!