What would be the best way to identify the secretomes in a list of proteins from a particular fungus that I have. Does downloading the secretomes of different fungi from Fungal Secretome knowledgebase and doing a blastp against the transcriptome of the fungus I have work? Or could somebody please suggest a tool or another method for the same using bioinformatics? Thank you for your time and consideration
Blasting your fungus just against secreted proteins may give you false positives in case some domains are present in both secreted and non-secreted proteins. I would rather go for reciprocal best hits (RBH: you blastp all proteins from species A (queries) against all proteins from species B (database). Then reverse: B proteins as queries, A as DB). And if you got annotations of B proteins (secreted vs non-secreted) you simply look at the results of these.
I expect that Fungal secretome DB may not have annotation for species closest to yours (lets name it X). If this is the case, and you are fond of scrapping the bottom of the barrel, you may increase sensitivity by picking say 3 proteomes located on the phylogenetic tree somewhere between X and some well annotated one (Y), then do the reciprocal blasting all against all. This is for picking X proteins having really weak/no hits to secreted Y ones, but which got RBH with other proteomes which in turn got RBH with secreted proteins from X. Can be easier to script than clearly describe...
The second option is to investigate databases of orthologues, i.e. http://phylomedb.org/ and intersect it with Fungal secretome. Meaning: you may get orthologues of secreted proteins in multiple fungal species with greater confidence than with your in house RBH first for say above-mentioned 3 (or more) species close to X. And then perform BRH X vs these 3 proteomes.
