It’s been an exciting and productive time since the PubMed Commons beta launch. We’ve learned a great deal, both here working under the hood and from the conversations in social media and blog posts.
We are working on answers to questions that people are asking, via our Twitter account and by revising and expanding information on the PubMed Commons page soon. And we will try out a Twitter chat: so keep your eye out on @PubMedCommons for the announcement.
There are now about 1,000 people signed up in the Commons. Remember, any author in PubMed can join, from anywhere in the world. Check out our step-by-step guide. Once you are in, you can invite others. So please spread the word!
What is a genome assembly?
The haploid human genome consists of 22 autosomal chromosomes and the Y and the X chromosomes. Each of the chromosomes represents a single DNA molecule, a sequence of millions of nucleotide bases. These molecules are linear, so one might expect that we should represent each chromosome by a single, continuous sequence. Unfortunately, this is not the case for two main reasons: 1) because of the nature of genomic DNA and the limitations of our sequencing methods, some parts of the genome remain unsequenced, and 2) emerging evidence suggests that some regions of the genome vary so much between individual people that they cannot be represented as a single sequence. In response to this, modern genomic data sets present a model of the genome known as a genome assembly. This post will introduce the basic concepts of how we produce such assemblies as well as some basic vocabulary.
Over the past several months, you may have noticed a warning message if you’ve accessed the NCBI site using Microsoft’s Internet Explorer web browser:
If you have been using Internet Explorer versions 7 or 8 (on “compatibility mode”) to surf the web, you may have seen this warning at the top of NCBI webpages.
This message has caused some concern among some users about exactly what changed on January 1, 2013 and whether or not they will still be able to access PubMed and other NCBI resources. We hope that this post will address some of the more common questions.