Specific gene annotation for genome assembly

Question

[aline.lucchetta]

Hi,

What should I do with a genome assembly to get gene CDS?

I'm new to bioinformatics and I'm working with Ambystoma mexicanum. The genome has just been released and I need only three annotated genes to run my codeml analysis. I'm looking into how to annotate the genes but I don't know if it would be the best approach. If it is, what are the first steps you recommend?

Thanks in advance

[GenoMax]

Do you have a close relative where you know the sequence of those three genes. If so you could take that sequence and try to identify homologs in your genome of interest using blast+ or blat.This recent thread has some pointers to to get you started: Finding a gene of interest in contigs from a transcriptome sequencing.

[aline.lucchetta]

Thanks for the suggestion but the problem is that my closest sequenced species has a peculiar genome that differs a lot from the rest, and also I need to access precisely the exons.

[GenoMax]

It looks like annotated transcriptome data from a recent Ambystoma mexicanum genome paper on is available here. You should be able to use that information. There is also a new genome assembly available in another paper in Nature.