Using NCBI Data and Tools for Your Research Project

Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project.   How and why do you use our resources? Check out the example below: Your professor has assigned you a research project looking at … Continue reading 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.
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NCBI Datasets: Easily Access and Download Sequence Data and Metadata

Effective May 2024, NCBI Datasets will replace legacy Genome and Assembly web resources  As part of our ongoing effort to enhance your experience and modernize our services, NCBI will gradually replace the legacy Genome and Assembly resources with the newly introduced NCBI Datasets resource. NCBI Datasets is a continually evolving platform designed to provide easy and intuitive … Continue reading NCBI Datasets: Easily Access and Download Sequence Data and Metadata

Only 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.

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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?).

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New & Improved NCBI Datasets Genome and Assembly Pages 

Legacy pages now redirect  Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.    The following pages have … Continue reading New & Improved NCBI Datasets Genome and Assembly Pages 

Download Assembled Genome Data Programmatically with NCBI Datasets

As previously announced, NCBI’s Assembly and Genome record pages will be redirected to new NCBI Datasets pages in June 2023. The NCBI Datasets Command Line Interface (CLI) tools provide easy, straightforward programmatic downloads of assembled genome sequence data. We invite you to check them out and let us know what you think!  Features & Benefits of NCBI … Continue reading Download Assembled Genome Data Programmatically with NCBI Datasets

Chapter 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.

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Gene Families and the Birth and Death of Genes