title: A comparative analysis of HGSC and Celera human genome assemblies and gene sets.
abstract: BACKGROUND
  Since the simultaneous publication of the human genome assembly by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics, several comparisons have been made of various aspects of these two assemblies. In this work, we set out to provide a more comprehensive comparative analysis of the two assemblies and their associated gene sets.
  
  
  RESULTS
  The local sequence content for both draft genome assemblies has been similar since the early releases, however it took a year for the quality of the Celera assembly to approach that of HGSC, suggesting an advantage of HGSC's hierarchical shotgun (HS) sequencing strategy over Celera's whole genome shotgun (WGS) approach. While similar numbers of ab initio predicted genes can be derived from both assemblies, Celera's Otto approach consistently generated larger, more varied gene sets than the Ensembl gene build system. The presence of a non-overlapping gene set has persisted with successive data releases from both groups. Since most of the unique genes from either genome assembly could be mapped back to the other assembly, we conclude that the gene set discrepancies do not reflect differences in local sequence content but rather in the assemblies and especially the different gene-prediction methodologies.
authors.affiliation: Tularik, Inc 112 Veterans Blvd, South San Francisco, CA 94080, USA.
authors.forename: Shuyu
authors.initials: S
authors.lastname: Li
authors.forename: Gene
authors.initials: G
authors.lastname: Cutler
authors.forename: Jane Jijun
authors.initials: JJ
authors.lastname: Liu
authors.forename: Timothy
authors.initials: T
authors.lastname: Hoey
authors.forename: Liangbiao
authors.initials: L
authors.lastname: Chen
authors.forename: Peter G
authors.initials: PG
authors.lastname: Schultz
authors.forename: Jiayu
authors.initials: J
authors.lastname: Liao
authors.forename: Xuefeng Bruce
authors.initials: XB
authors.lastname: Ling
mesh_terms: D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*