I've got a dozen different strains of bacteria for which we've sequenced the whole genomes of (we have paired end reads - forward and reverse - for each strain). I wish to find and locate a specific house keeping gene in each strain.
Could I convert the fastq files into fasta files, set up a blast database containing the fasta short read files and then blast the query gene sequence against those? Or would I need to assemble each genome first and then make a database out of the assemblies and then blast the query gene sequence against those?
Would appreciate your input, thanks :-)