I have two genome assemblies for one species that is polymorphic with respect to colour and a list of genes of interest.
I want to extract the contigs from each assembly that map to a gene of interest, call it gene X.
The way I was thinking of doing this, is by blasting the each assembly against a database containing only the gene of interest in reptiles (my assembly is a snake genome). My goal is to then align the contigs from each assembly that map to gene X and look for mutations.
I know how to limit the query to just a certain taxon (see below), but I'm not sure how to specify just a single gene or if this is possible.
Any constructive input is highly appreciated!
blastn -db refseq_rna -entrez_query="reptilia[ORGN]" \ -query contigs.fsa -out hits.out -remote \ -word_size 11 -gapopen 5 -gapextend 2 \ -penalty -3 -reward 2 -evalue 0.00001 \ -num_descriptions 3 -num_alignments 3