How to perform synteny alignments and plots only with a gene?

Question

[Rafael Soler]

Hi everyone,

I'm trying to perform synteny alignments and plots for a gene of interest and its exons. I have two genomes in FASTA format and their corresponding annotations in GFF3 format.

Does anyone know some software that can help me with this? Ideally, I would like to visualize the alignment in synteny blocks, as well as highlight the exons and their positions in both genomes. Something similar to this:

Any help or advice would be greatly appreciated!

Thank you.

[Rafael Soler]

hugo.avila Ming Tommy Tang Thanks for the recommendations, but these tools are developed to visualize rearrangements at the chromosome scale, but I am interested in doing this type of graph at the single gene scale.

[hugo.avila]

I understand, but I believe that both tools can still be used to work with single genes if you provide the right labels, links, and coordinates. Essentially, you would be inputting smaller alignments than you would if you were working with chromosomes, so it should work.

Additionally, I believe that pyGenomeviz has some single gene examples on their GitHub page, such as the one shown in the image below:

One of these tools can be modified to suit your needs. Alternatively, you can also try gggenes. Maybe they have what you're looking for. However, don't limit yourself to gggenes; the gg group of tools has many features for plotting genomic data.

Answer 1

[cmdcolin]

i try to collect many different visualization tools, here are those tagged 'comparative' https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Comparative

I'm not sure if any exactly match your needs out of the box, but you may be able to find something that can help

[Rafael Soler]

Thanks for the repo! It is difficult as all the tools are design for chromosomal scale.

[cmdcolin]

if you want a 'genome browser' type approach, could try jbrowse 2, I am a developer of it. it has pairwise synteny visualization features like you are interested in, and you can zoom in on regions of interest, export as svg, etc. our quickstart guide shows how you can get started https://jbrowse.org/jb2/docs/quickstart_web/#adding-a-synteny-track-from-a-paf-file just one option and it's admittedly a somewhat complex system to administer and less 'scriptable' than R perhaps, but could be an option

[Rafael Soler]

Thanks for the info! So valuable!

Answer 2

[Ming Tommy Tang]

take a look at https://github.com/schneebergerlab/plotsr

Answer 3

[hugo.avila]

Hello try this https://github.com/moshi4/pyGenomeviz