# How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the nucleotide sequences corresponding to the gene between the two samples. My goal with this is to count how many single-base differences there are in each gene. However, I'm not sure how to match the sequences in the assembly to known reference sequences (by the way is there a good resource to download all of these at once?) for C. Elegans genes.

My thought was to run BLAST between the reference sequence and each genome and find the match with the best score, if any. Is this a reasonable approach, or is there some better way to do this?

2. Use a tool that can model introns and exons to map a protein into a genome. I haven't worked in this field in more than 10 years now, so it is very likely that there are other programs around today, but back in the day, I would do this using either exonerate or genewise. With exonerate, the command would be:
exonerate -m protein2genome -n 1 -t assembly.fasta -q allproteins.pep > out