Hi,
What is the easiest way to annotate a genome that has no annotation. I've the genome and annotation of a very related species.
In final, I wan to have the same structure as refGene.txt and ensGene.txt from UCSC.
Here's an example from the RAT ensGene.txt :
585 ENSRNOT00000044270 chr1 + 5472 16844 5472 16844 8 5472,5523,8281,8991,10768,14683,15968,16733, 5485,5725,8567,9795,10993,14807,16732,16844, 0 ENSRNOG00000021490 incmpl incmpl 0,1,2,0,0,0,1,0,
585 ENSRNOT00000049921 chr1 + 5525 16968 5525 16968 8 5525,8275,8991,10768,14677,15965,16733,16943, 5725,8567,9795,10993,14807,16732,16846,16968, 0 ENSRNOG00000021490 cmpl incmpl 0,2,0,0,0,1,0,2,
585 ENSRNOT00000051735 chr1 + 5525 16968 5525 16968 7 5525,8275,8991,10768,15965,16733,16943, 5725,8567,9795,10997,16732,16846,16968, 0 ENSRNOG00000021490 cmpl incmpl 0,2,0,0,1,0,2,
My strategies is to download all the gene (CDNA ?) from ensembl and ucsc from this related species and to map with gmap them on the unannotated genome. Is it a good way to do this ?
Thanks a lot,
N.
•
written
by
Nicolas Rosewick
1 answer
yes, basically you can follow the similarity-searching-based (map proteome of relative species to your genome assembly) method. And you can also try some de novo gene prediction approaches. Then, it is good to combine the two different strategies (this can be done using some combiners, e,g,, EVM, glean, Maker ...).
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