Specific gene annotation for genome assembly
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
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aline.lucchetta •
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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.
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.
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.