looking for a way to identify a specific gene, and in varying numbers across multiple genomes.

Question

[goatsrunfaster]

I am looking for a way to identify a gene (or more specifically a sequence), and the number of those sequences across a number of bacterial isolates. Assuming I have the sequence. What is the best way to do that? Are there any tools specifically built for finding a user-supplied sequence across a large number of genomes? Note this sequence is not highly studied so there is no tool already available.

Answer 1

[oakhamwolf]

If you have access to the genomic sequences of the isolate, could you just make a BLAST database out of them and search for your sequence that way?