Does anyone know where to find and download information on genome size and number of protein-coding genes for as many eukaryotes as possible? I found small sets in Ensembl! and JGI but I suspect there must be more sequenced species. So far, I have the full set of fungi, about 40 mammals and some inverterbartes.
The NCBI has a summary site at http://www.ncbi.nlm.nih.gov/genome/browse/, and you could look at genomesonline.org (which I think is also run by the JGI, but certainly should have more than 40 species).
Thanks Minou! It's exactly what I was looking for. But after I had a look at this page (with the summary in NCBI) I'm even more puzzled. Yes, the information is there, but it's so much contradictory! Different projects end up with numbers with huge deviations, up to 2 times. The number of proteins in some cases is the number of transcripts, which can be justified but I'm only interested in the corresponding genes and the number of genes can include the non-coding genes... I'm not sure the information is useful without careful reading about each and every project - at least for the higher eukaryotes. Which brings me to the thoughts about the strandards in data submission: would be nice to really follow them!
Hi Ekaterina, I agree, some more unified standards would be nice. When I used the data for some summary information, it needed lots of manual checking. I guess the problem is that the field is moving forward fast, and assembly types and annotation standards ("styles") have changed rapidly over the last few years (e.g. gene predictions without UTRs were the rule before RNA seq, but now using RNA seq for gene annotation with de novo genomes becomes standard).
Yes, you're right. I guess I'll have to go for manual check, don't see any way to make it automatical. Thanks again!
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