Mouse Genome Assembly NCBI m37

Ensembl Mouse is based on the NCBI m37 mouse assembly (April 2007, strain C57BL/6J). For release 47 the gene annotation presented has been a combined Ensembl-Havana geneset, which incorporates more than 15,000 full-length protein-coding transcripts annotated by the Havana team in addition to the Ensembl automatic gene build. The mouse genome sequence is now considered sufficiently stable that since September 2006 the major genome browsers have come together to produce a common set of identifiers where CDS annotations of transcripts can be agreed and these identifiers are also shown.

Mouse Genome Assembly NCBI m36

Ensembl Mouse is now based on the NCBI m36 assembly. Additional known and novel genes are included in this build; 95% of the known genes and 68% of the novel genes from build m34 retain the same Ensembl gene ids in this release. More information is available from Ensembl Mouse.

Mouse Genome Assembly NCBI m35

Ensembl Mouse is now based on the NCBI m35 assembly, released in December 2005. Additional known and novel genes are included in this build; 95% of the known genes and 68% of the novel genes from build m34 retain the same Ensembl gene ids in this release. More information is available from Ensembl Mouse.

Mouse Genome Assembly NCBI m34

The Ensembl Mus musculus is now based on the NCBI Mouse Build 34, released 17 May 2005. Gene annotation - Added new non-coding gene annotation based on RFAM domains

Mouse Genome Assembly NCBI m33

This release provides a full Ensembl gene build for the NCBI m33 mouse assembly (freeze May 27, 2004). After extensive QC, principally from the Sanger Institute, most artefactual assembly issues introduced in build m32 have been removed. The whole genome N50 is 22.3 Mb. (Build m32 was 17.7 Mb).

New software systems have improved the gene set. More than 85% of genes from build m32 retain the same Ensembl gene ids in this release. New gene identifiers were assigned where a many-to-one or many-to-many mapping of old genes to new gene structures was detected.

The interpolated mouse map will be included in the next release and patches to the build will be provided regularly as more detailed analysis is performed.

New core, est and estgene databases built on the NCBIM33 assembly. New SNP and lite databases.

Ensembl pre-release: Mouse NCBIm33

We are pleased to announce the release of the NCBI m33 assembly of the mouse genome.

Build 33 (freeze May 27, 2004) has undergone extensive QC, principally from the Sanger Institute. Most of the artefactual assembly issues introduced in build 32 have been removed. The whole genome N50 is 22.3 Mb (compared to 17.7 Mb from Build 32).

Mouse build 33 represents a composite assembly made by merging HTGS phase 3 sequence with the Mouse Genome Sequence Consortium v3 Whole Genome Shotgun Assembly (MGSCv3). The assembly was performed by NCBI using a 'combined' tiling path that was largely created automatically, but was manually curated in places. This facilitated placing finished sequence in the context of the MGSCv3. Draft sequence was not included in this build as the slight increase in coverage one gains by using this is offset by the increase in build errors.

As this is a pre-release, the database only contains repeat analysis, ab initio gene predictions, and BLAST comparisons. The Ensembl gene prediction pipeline is in progress, and no complete Ensembl gene predictions are available yet. The annotated assembly will be released on the main Ensembl site (http://www.ensembl.org/), currently planned for the start of September 2004.

New NCBI30 assembly

New NCBI30 assembly, gene build, and estgenes for Mouse NCBI30 is a composite assembly built using the MGSCv3 Whole Genome Shotgun assembly and High Throughput Genome Sequence (HTGS). A conservative approach was taken in the construction of this assembly:

• Only HTGS phase 3 sequence was used

• Only C57BL/6J sequenced was assembled

• The MGSCv3 was used as a tiling path file

• SNP datasets have been updated to dbSNP112

The Measure Of Man

Published this week in Nature, mouse genome dictionary identifies 1200 new genes in the human book of life The sequence and analysis of more than 95 percent of the mouse genome is published for the first time in today's edition of Nature (5 December). In addition to revealing 9000 new mouse genes, the research papers reveal 1200 new human genes, a significant number of which are likely to be involved in cancers and other diseases. These findings will allow researchers to home in more rapidly on genes in order to better diagnose and treat many human diseases.

International consortium maps 98% of the mouse genome

A UK-US-Canada consortium coordinated at the Wellcome Trust Sanger Institute publishes in Nature online the most comprehensive map of the mouse genome, containing an estimated 98% of the DNA sequence. The map has already proven a valuable resource in the hunt for mouse and - even more importantly - human genes.

Draft Sequence of Mouse Genome

In a landmark advance in genomics, the international Mouse Genome Sequencing Consortium today announced that it has assembled and deposited into public databases an advanced draft sequence of the mouse genome - the genetic blueprint for the most important animal model in biomedical research.

Ensembl Mouse v3 Released

The Mouse Genome version 3 has been released with 96% coverage of euchromatic genome. This was the result of whole genome shotgun and its subsequent assembly. Ensembl has a confirmed prediction of 22,444 genes across the genome and around 75% have a direct homolog in human.

Ensembl Mouse Assembly v 1 Released

The first MGSC mouse genome assembly is ready, and has been annotated through the Ensembl pipeline. The 3.1.1 mouse site presents this data, which is based on pure whole genome shotgun data of ~4x coverage, frozen in October 2001. The WGS assembly was aligned to the joint Sanger/St Louis BAC map (frozen in Sept 2001 - details) to provide this assembly. BAC-based sequencing has not been incorporated. The assembly was run through the normal Ensembl pipeline to predict genes and other features of interest. (statistics)

Deeper (5.5x) shotgun coverage, improved assembly software, better BAC maps, and more sensitive gene prediction will improve these data over time. We expect updates at ~3 month intervals, and will keep people informed of progress on the ensembl-dev mailing list.

Credits for the mouse sequencing project can be found here.

Mouse Ensembl released with FPC based assembly

The web site mouse.ensembl.org shows the mouse physical map assembly based around clone fingerprints (see below for credits and details), and, where retrievable sequence information. For draft and finished clones, the Ensembl automatic annotation system has been run and provides predictions of genes in these regions.

The FPC map covers an estimated 95% of the genome (as clones) and many clones have BAC-end sequences providing a integrated and useful resource for mouse mapping projects.

At the sequence level around 350MB (with redundancy), representing an estimate of about 10% of the genome is large scale sequenced clones. On this DNA we have confirmed 15,694 genes, which is an inflated number due to both redundancy at the DNA level and fragmentation between pieces of DNA.

We expect to see radical improvements to the types of data, the quality of data and its subsequence annotation over the next three or so months, in particular the integration of this data with the whole genome shotgun. We are releasing this current data early as a resource to the community and are working hard on many aspects, including omprehensive mouse to human linkage.

The Ensembl project is an entirely open software project supported by the Sanger Centre and the EBI, part of EMBL. The majority of its funding is from the Wellcome Trust.

Mouse Map Credits

7,500 clone contigs assembled by fingerprinting by Marra et al. (Genome Sequence Centre, BC Cancer Research Centre, Vancouver) were extended and joined to form <600 contigs covering approximately 90% of the mouse genome. Mouse BAC end sequences from TIGR (Zhao, et al.) were used to align the mouse contigs to the human genome to accelerate the manual joining process. The synteny information was not used, however, to create joins. 6,800 markers from radiation hybrid and genetic maps of the mouse were integrated into the database to confirm contig order and orientation. For more details see Gregory et al. Further refinement of the map is in progress at the Sanger Centre and Washington University (McPherson, et al).

Of Mice And Men

The Mouse Sequencing Consortium (MSC), announced today (Tuesday 8th May) that it has completed the first phase of reading the mouse 'book of life', reaching its goal on time and within budget. The $58 million (£40 million) collaboration on the mouse genome was initiated in October 2000 and has taken just 6 months to generate '3x' coverage - where each of the 3 billion 'letters' of the genome is 'read' three times. The sequence now covers an estimated 94% of the mouse genome.

Mouse Genome Data Available in Public Databases

A public-private effort to accelerate the sequencing of the mouse genome has exceeded its own goal of achieving 66 percent coverage of the genome just three months into the six-month project. At its current pace, the Mouse Sequencing Consortium (MSC) expects to reach its target of three-fold coverage by April of this year.

Public-Private Consortium Accelerate Mouse Genome Sequencing

The National Institutes of Health, the Wellcome Trust and three private companies today announced they have formed a consortium to speed up the determination of the DNA sequence of the mouse genome. The Mouse Sequencing Consortium will provide $58 million over the next six months to decipher the mouse genetic code.