Make a database and search inside the database with blastn, for example.

1) First you need to make a database from your nucleotide sequences.

To do this:

makeblastdb -in input_file (file-name of the contigs or whatever) -dbtype nucl (if nucleotide) -out dbname (the database name)

Use input file in *.fa-format.

2) Run the blast-program:

blastn -query input (with the gene file) -db (database name, which was created in step 1) -out outname (file name with the results)

So use blastn for this search in the nucleotide database. You said you know the sequence of needed gene in the genome?

Hopefully the size of the database will not be the bottle neck.

Good luck!