gene alignment (microsynteny)
1
1
Entering edit mode
8 months ago
gubrins ▴ 350

Hi all,

I have two reference genomes already annotated and I want to study several genes that are found in a tandem array, to see if they are orthologous or not and if a specific gene in species A originated several others in species B. I am not finding any tool for doing that, as the ones I found are specifically focused on macrosynteny (as chromosomal rearrengements).

I tried to align the genomic sequences containing those genes, but the genomic sequences are in fasta files, so they are missing the gene information. How could I add the gene information (for both species) to that alignment if there is no tool that can do it?

Thanks in advance!

alignment microsynteny • 487 views
ADD COMMENT
2
Entering edit mode
8 months ago
cmdcolin ★ 4.0k

I am not an expert in these methods, but this is a random list of ideas

you can look at this guide for mcscan which performs a protein-alignment of all genes https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)#microsynteny-visualization

this gives you just a gene-level view of microsynteny. I sometimes see the mcscan method called gene based or marker based alignment

if you want to see the per-base level alignment, that is often a "whole genome alignment". minimap2 is a common example of this

then there are perhaps hybrid methods, like AnchorWave. you can see that the steps of anchorwave uses first marker/gene based alignment, then uses those to extend the whole genome alignment. this was i believe successfully used in plants especially

https://github.com/baoxingsong/AnchorWave

then you can try to visualize results, which i think is a very interesting challenge. many tools do large scale visualizations like circos and syri but indeed, zooming in and getting microsynteny visualizations is useful

I develop jbrowse 2, which i think has some unique capabilities for zooming in and viewing alignments. you can follow the quickstart guide that includes loading a PAF file from minimap2 here https://jbrowse.org/jb2/docs/quickstart_web/#adding-a-synteny-track-from-a-paf-file

I also know there are lots of other tools, depending on your interest and I catalog them here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Comparative

ADD COMMENT

Login before adding your answer.

Traffic: 1338 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6