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ENSEMBL ANNOTATION OF HUMAN GRCh37. Better algorithms for a better human.
J. Fernandez-Banet1, B. Aken1, S. Fairley1, M. Ruffier1, M. Schuster2, S. Searle1, A. Tang1, J. Vogel1, S. White1,
A Zadissa1, T. Hubbard1.
Wellcome Trust Sanger Institute1 and European Bioinformatics Institute2, Wellcome Trust
Genome Campus, Cambridge, CB10 1SA, UK.
In February 2009 the Genome Reference Consortium released a new human genome
assembly, GRCh37. This new assembly improved the general quality of the whole genome
sequence. In addition it also includes alternative assemblies for a number of haplotypic
regions.
EnsEMBL aims to produce a set of annotation rapidly, whilst at the same time introducing
new algorithms that improve its quality.
Traditionally Ensembl has only used protein to genome alignment to build CDS structures
with UTR added from cDNA alignments. Here we present how combining the models
obtained from protein alignments with those obtained from cDNAs using exonerate's
cdna2genome model has helped us produce a more refined gene set which exactly matches
a higher percentage of the protein sets distributed by RefSeq and SwissProt databases.
The introduction of a higher number of haplotypes for GRCh37 added an extra level of
complexity to the gene annotation process as only the best alignment for each individual
sequence gets selected for gene annotation. We have developed a method to project the
annotation between the reference chromosome and the haplotypes described for the same
region improving the number of models build in non reference sequences, and making it
possible to link alternative alleles of genes.
Custom methods have been used to annotate immunoglobulins and selenocysteine
containing genes.
The CCDS gene set and manual annotation from Havana have also been incorporated in the
annotation set.
The quality checks performed in EnsEMBL human annotation for GRCh37 show it as our
highest quality annotation on a human genome to date.