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Assembly
The UMD 3.1 assembly (NCBI assembly accesion
GCA_000003055.3),
released in December 2009, is the third release of the cow (Bos taurus) assembly from the
Center for Bioinformatics and Computational Biology (CBCB)
at University of Maryland. The genome sequences were generated using a combination of BAC-by-BAC hierarchical (~11 million reads)
and whole-genome shotgun (~24 million reads) sequencing methods, assembled using the Celera Assembler version 5.2.
The total length of the UMD3.1 assembly is 2.65Gb. The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size for contigs in the UMD3.1 assembly is 103785.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003055.3
Download Cow genome sequence (FASTA)
Previous assemblies
Annotation
Gene annotation in cow has been generated by alignment of proteins from three major sources (in descending order of their contribution to the final gene set):
- Bos taurus (cow) proteins from UniProtKB and NCBI RefSeq and Bos taurus cDNAs from INSDC. For proteins, UniProtKB proteins were filtered to keep only those of protein existence (PE) levels 1 and 2 (i.e. with protein or transcript level evidence), and only curated RefSeq proteins (accessions starting with "NP_") were used. For cDNAs, they were also filtered to keep curated RefSeq mRNAs (accessions starting with "NM_") and to remove those associated with PE level 3-5 UniProt proteins.
- UniProt mammalian and vertebrate proteins of PE levels 1 and 2; and
- Translations of Ensembl human genes which have one-to-one orthologues in mouse (taken from Ensembl release 62 data).
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