Category Archives: Genome
Using NCBI Data and Tools for Your Research Project
What is the “dark matter of the genome”?
The phrase "dark matter of the genome" is used by scientists who are skeptical of junk DNA so they want to convey the impression that most of the genome consists of important DNA whose function is just waiting to be discovered. Not surprisingly, the term is often used by researchers who are looking for funding and investors to support their efforts to use the latest technology to discover this mysterious function that has eluded other scientists for over 50 years.
The term "dark matter" is often applied to the human genome but what does it mean? We get a clue from a BBC article published by David Cox last April: The mystery of the human genome's dark matter. He begins the article by saying,
Twenty years ago, an enormous scientific effort revealed that the human genome contains 20,000 protein-coding genes, but they account for just 2% of our DNA. The rest of was written off as junk – but we are now realising it has a crucial role to play.Read more »
NCBI Datasets: Easily Access and Download Sequence Data and Metadata
Posted by assembly, Comparative Genomics Resource (CGR), Genome, NCBI Datasets, What's New
inOnly 10.7% of the human genome is conserved
The Zoonomia project aligned the genome sequences of 240 mammalian species and determined that only 10.7% of the human genome is conserved. This is consistent with the idea that about 90% of our genome is junk.
The April 28, 2023 issue of science contains eleven papers reporting the results of a massive study comparing the genomes of 240 mammalian species. The issue also contains a couple of "Perspectives" that comment on the work.
Read more »How many genes in the human genome (2023)?
The latest summary of the number of genes in the human genome gets the number of protein-coding genes correct but their estimate of the number of known non-coding genes is far too high.
In order to have a meaningful discussion about molecular genes, we have to agree on the definition of a molecular gene. I support the following definition (see What Is a Gene?).
Read more »New & Improved NCBI Datasets Genome and Assembly Pages
Download Assembled Genome Data Programmatically with NCBI Datasets
Posted by assembly, Comparative Genomics Resource (CGR), Datasets, e-utilities, EDirect, Genome, What's New
inChapter 7: Gene Families and the Birth & Death of Genes
This chapter describes gene families in the human genome. I explain how new genes are born by gene duplication and how they die by deletion or by becoming pseudogenes. Our genome is littered with pseudogenes: how do they evolve and are they all junk? What are the consequences of whole genome duplications and what does it teach us about junk DNA? How many real ORFan genes are there and why do some people think there are more? Finally, you will learn why dachshunds have short legs and what "The Bridge on the River Kwai" has to do with the accuracy of the human genome sequence.
Click on this link to see more.
Gene Families and the Birth and Death of GenesPosted by alternative splicing, Genome, junk DNA, What's in Your Genome
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