How can I compare two reference genome

Question

[yasmint]

Hi everyone,

I am working on gonadal transcriptimes in lamprey. Two reference genomes are available for the species. There are differences in the number of genes in two assemblies but the annotations are poor. I want to find out which genes are expressed in my sample but missing in one of the genomes. How can I do that? I would really appreciate your suggestions.

Thanks, Tamanna

[cpad0112]

1. Make a list of genes from annotations, unique to each assembly
2. Intersect the differentially expressed gene list with these two lists.

Answer 1

[colindaven]

I like to do this kind of analysis on sequence level, as it likely more robust than the annotations

You can

• extract gene sequences from both assemblies in FASTA format
• use a tool such as proteinortho to blastn them against each other https://www.bioinf.uni-leipzig.de/Software/proteinortho/
• view the list of identifiers as a CSV together

You can also include identifiers from a closely related species if one exists

Answer 2

[Antonio R. Franco]

Give a try to programs like Mauve