<p>The Homo sapiens Genome (Build 37.2) has just been published by the NCBI : <a href='http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=9606&amp;build=37&amp;ver=2'>http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=9606&amp;build=37&amp;ver=2</a></p>

<p>Do the Fasta sequences of the human genome have changed since the version 37.1 (e.g: some large contigs of NNNNN would have been solved  ? )  or is it just a matter of annotations ?</p>

<p><strong>Short answer</strong></p>

<p>Afaik, the sequences are not changed for the <em>primary assembly</em>, so if you don't go looking for the new sequences, you won't find them. However, some new corrections and new sequence are available if you want them. The annotations have been updated.</p>

<p><strong>Long answer</strong></p>

<p>NCBI 37.2, like Ensembl 60, is based on GRCh37.p2.</p>

<p>GRCh37.p2 is, as the name implies, just a patch release for GRCh37. It contains two kinds of patches, which should be seen as temporary updates until they are fully incorporated into the next major release of the genome.</p>

<ul>
<li>A fix patch represents corrections to an existing sequence.</li>
<li>A novel patch represents novel sequence (perhaps filling some of the N's of runs).</li>
</ul>

<p>As I understand it, these are not intended to replace the original sequences while the main release, GRCh37, is still in effect. They can be seen as a sneak preview of the next major release for those who are interested. This means that the GRCh37 <em>primary assembly</em> is the same between GRCh37, GRCh37.p1 and GRCh37.p2, and the patch sequences exist separately.</p>

<p>If you download the primary assembly sequence for Chromosome 5, say, from the <a href='ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p2/'>GRC</a>, you will get the original sequence, which doesn't include the updates. To get the updated sequences, you would need to download a separate patch file. Small annotation files are also provided that explain where the patch sequence "fits" in the original sequence.</p>

<p>Ensembl follows the pattern of keeping the original sequences separate from the patches - you would <a href='ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/'>download</a> the original sequences separately from the patch sequences.</p>

<p>I'm less sure of this, but I think NCBI also keeps the sequences separate. NCBI 37.2 contains a 'GRCh37.p2-Primary Assembly', and the patch sequences seem to be represented as a separate assembly - "GRCh37.p2-PATCHES".</p>

<p>Note also that GRCh37.p2 contains the mitochondrial sequence - previous versions of the assembly did not contain this.</p>
