I'm trying to create a figure which visualizes the locations of NBS-LRR genes on chromosome 1 on the watermelon genome based on the watermelon sequencing genome paper here. Essentially, I want to create a chromosome map of locations of specified genes for a figure.
I've tried to set up the watermelon genome as a database for BLAST, and while it did give me the numeric location of these genes on the watermelon genome, it doesn't do a good job with "visualizing" where the genes lie on the chromosome.
I'm thinking about using bowtie to align these sequences to chromosome 1 and then visualizing their locations and alignment in IGV. But can bowtie be used for aligning single "reads" of a very large size to a chromosome?
Can anyone suggest a program or tool to create a chromosome map of specified genes given the target genome and DNA sequences of interest? Thank you!