Using IGB to visualize a gene from multiple species at the same time

Question

[nash.claire]

Hi

I was wondering whether it is possible to use IGB to view a gene of interest from mutliple species in the same browser at the same time? Ideally I'd like to zoom in on my gene of interest and have multiple species lined up and then afterwards load a BED file of other regions of interest we have to compare to multiple species at the same time.

Would this be possible?

[nash.claire]

Thank you very much genomax2! I'll give it a shot.

Answer 1

[GenoMax]

You can download conservation track from UCSC browser as a WIG/MAF format file here (at least for vertebrates, not sure what species you are interested in, scroll down on the page to find download links).

Integrated Genome Viewer (IGV) supports both formats so it should be possible to do what you are asking for. IGB appears to support only WIG format so you would need to give it a try and see if that works. Having your genome aligned to UCSC reference may be a pre-req for this to work right. If you were using Ensembl reference then perhaps BioMart can be used to export the alignments of genes you are interested in. More info about comparative genomics at Ensembl is in their FAQ.

Alternatively you can check the homologene record of the gene you are interested in @NCBI and download/see the MSA's. You can then open them in an MSA editor for local examination.