Another option, create a custom selection of GenBank sequence records that you want to find in your data and do a web-based/local BLAST.
Best, Thijs
Hi Glory,
What format is your whole genome sequence in?
If your species is on the Ensembl Fungi database (https://fungi.ensembl.org/index.html) then this will make things easier as you can use their BLAST tool.
If not, but there is an accession number to the genome then you can search this. In NCBI Blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) you can tick the box labelled "align two or more sequences" and then you can restrict your BLAST to just the gene you are interested in, and the genome of that species. You can also do a BLAST where you restrict to a species name by typing the name of the species in the ORGANISM box - this will ensure hits are only against that species.
If the genome that you have is not on Genbank or Ensembl then, as Matthijs says, you can set up a standalone BLAST. This is not too difficult to do, but if you have no experience of it, or no one to help you then it might be tricky. It is explained here https://www.ncbi.nlm.nih.gov/books/NBK52637/.
Once you have this set up then you have all the BLAST functionality (Blastn, tBlastn etc.) against the genome.
Good luck!
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