Which tool would you use to compare a de-novo created genome against a better-annotated reference genome to identify the gene positions of this first newly created genome?
Would this also work on a transcriptome? or do one need genomic sequences?
thanks
You can do it at the proteome level - compare the proteins that the two genomes encode. Proteins structure conservation has a much better power of detection compared with nucleotide sequences. Check out our tool: http://pqi-list.org/
Laurence Stuart Dawkins-Hall
- I'm not sure what to do with the link. I know ensembl and I have worked a lot with several tools of it, including BLAT ( as for genome comparisons). But I'm not sure which tool you meant here. I am not looking for a mining tool. I would like to compare a draft genome with a well ( or maybe better annotated) genome, to try and extract the genes from the draft genome. Did you think of anything specific?
Jan Zaucha this is true and I was thinking of that, but for that i first need to get the proteome, which I don't have as well. I'll look into the tool though. thanks
In that case I am not familiar with any tool that will fully automate your task. You can align your genomes with mummer http://mummer.sourceforge.net/ and check what proportion of the genes you are recovering...
AUGUSTUS (https://github.com/Gaius-Augustus/Augustus) offers a mode for comparative genome annotation. One feature is that annotations from (one or several) reference organisms can be “projected” to the new genome. Another option is to de novo annotate a number of genomes, simultaneously.
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