In class, the professor said that there is about 8% of protein-coding genes in human. I wonder how biologists estimate this without annotating all of human genes. Thank you!
S/he's off by about 6 - 7%.
As per the national human genome research institute approximately 1% of the human genome encodes proteins. We can tell this by looking at the sequence (which we're now able to do quite quickly) and identifying those portions of the sequence can be translated to protein using the genetic code.
Scientists have been able to identify approximately 21,000 protein-coding genes, in large part by using the long-ago established genetic code. But these protein-coding regions make up only approximately 1 percent of the human genome...
It is important to remember that protein-coding genes have a start and an end, exons and introns, and identifiable promotors. Knowing that these factors exist and how to identify them (usually by their unique DNA sequences, the frequency they occur and their sequence lengths) we can identify these sequences as part of whole genome analyses.
Next-generation sequencing made it possible to sequence the entire genome of a human in a matter of days, if not hours. This massive database makes it possible to identify it's variable elements. Now, knowing where a promotor is, the following start codon of a gene can be found along with its stop codon. This leads to identifying open reading frames (ORFs).
Now it is simple, in that simply counting all the ORFs in relation to the other structural and "nonsense" DNA and the percentage of protein coding sequences can be determined. Remember that this is the norm, however there is still much we do not know about the human genome. There may be more protein-coding genes with unknown promotors that we do not know of. So always keep on asking!