November 2012, Human Annotation Release 104

Full annotation run for assemblies:

• GRCh37.p10 (accession GCF_000001405.22)
• CHM1_1.0 (accession GCF_000306695.1)
• HuRef (accession GCF_000002125.1)
• CRA_TCAGchr7v2 (chromosome 7; accession GCF_000002135.2)

Announcement: To avoid confusion between the independent notions of a genome assembly and its annotation, NCBI is now using Annotation Release numbers to designate annotation versions. Human Annotation Release 104 reflects this change; the old nomenclature style would designate this as "NCBI build 37.5".

Annotation Release numbers:

• are integer values that increment each time the genome annotation is updated.
• have initial values starting at 100 or higher.
• are incremented independently for each organism. This means that different organisms may have the same release number (e.g., Human 105, Mouse 105), but the two annotation runs are not connected. In addition, differences in the release number for different organisms does not imply one annotation release is more up-to-date than another (e.g., Mouse 104 could be a newer dataset than Human 105).
• are used for the set of annotations calculated on one or more genome assemblies for the same species. For instance, Human Annotation Release 104 includes annotation for a new alternate assembly, CHM1_1.0, and updated annotation for the reference assembly, HuRef assembly, and the CRA_TCAGchr7v2 chromosome 7 assembly.

Therefore, a specific genome annotation dataset is associated with three primary identifiers: the assembly accession, the annotation release number, and the NCBI taxonomy ID or species name.

November 2012 Update: NCBI released an update for the human genome annotation. The chromosome sequence is unchanged, but additional incremental updates released by the Genome Reference Consortium (GRC) as Fix or Novel Patches (Assembly GRCh37.p10) are included. Genomic regions with corresponding alternative loci or patches are reported in the Assembly regions track. A previous version of the reference genome assembly, NCBI Build 36.3, can still be accessed for Map Viewer display and for BLAST. For additional information about NCBI's genome annotation pipeline, Map Viewer, release notes for this annotation release, statistics, and the status of the CCDS project please refer to:

• Release Notes: release notes for this annotation release
• Statistics: statistics for this annotation release
• CCDS Project: current status of international Consensus CDS annotation project
• Map Viewer Help: details about navigation and customizing your display
• GRCh37.p9 Assembly report: description and statistics on the genome assembly structure
• Annotation Information: description of features annotated by NCBI's eukaryotic genome annotation pipeline
• Gnomon: description of NCBI's Hidden Markov Model (HMM) ab initio prediction program

The NCBI Map Viewer provides graphical displays of features on the human reference genome sequence assembly maintained by the GRC and the alternate HuRef genome assembly, as well as cytogenetic, genetic, physical, and radiation hybrid maps. Map features that can be seen along the sequence include genes, transcripts, NCBI contigs (the 'Contig' map), the BAC tiling path (the 'Component' map), STSs, FISH mapped clones, ESTs and transcripts from several different organisms, Gnomon predicted gene models, and more.

You can find genes or markers of interest by submitting a BLAST query against the genome, or a text query against the whole genome or a single chromosome. Use the Advanced Search form for more complex queries. Results are indicated both graphically, as tick marks on the ideogram, and in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes the Gene, Ab initio (i.e., the Gnomon predicted models), and UniGene sequence maps. You can also browse a chromosome by clicking on a chromosome link in the ideogram above. Use the "Maps & Options" window, available on individual chromosome displays, to configure your display.

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