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Bioinformatics Vol. 19 no. 13 2003
Pages 1597-1605
© 2003 Oxford University Press

A comparative analysis of HGSC and Celera human genome assemblies and gene sets

Shuyu Li 1,{dagger}, Gene Cutler 1,{dagger}, Jane Jijun Liu 1,{dagger}, Timothy Hoey 1, Liangbiao Chen 2, Peter G. Schultz 3, Jiayu Liao 3,* and Xuefeng Bruce Ling 1,*

1 Tularik, Inc. 112 Veterans Blvd, South San Francisco, CA 94080, USA, 2 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China and 3 The Genomic Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA

Received on December 21, 2002 ; revised on March 11, 2003 ; accepted on March 26, 2003

Motivation: 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.

Contact: xling{at}tularik.com

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


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