Visualize location of genes on Chromosomes

Question

[kevluv93]

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!

[jotan]

You wouldn't need a bowtie alignment if you already have the genome coordinates from BLAST. Can you not just upload the genome coordinates of the genes you're interested in?

Answer 1

[Jean-Karim Heriche]

Have a look at genoverse (code on GitHub).

Answer 2

[h.mon]

You can do what you want with both Spaln and GMAP. Both output GFF3 and SAM, so the results are easily viewed on IGV. Bowtie is not a good fit for this task indeed.

Answer 3

[Alex Reynolds]

If you're making a web figure, this AngularJS directive might be useful.