Nucleic Acids Research, 2002, Vol. 30, No. 22 5004-5014
© 2002 Oxford University Press
Comparison of whole genome assemblies of the human genome
1 Department of Computer Science, Washington University and 2 Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA and 3 University of Michigan School of Medicine, Medical Science Building II, Room 5622A, Ann Arbor, MI 48109, USA
*To whom correspondence should be addressed. Tel: +1 734 615 5510; Fax: +1 734 615 6553; Email: dstates{at}umich.edu
Present address:
Eric C. Rouchka, University of Louisville Department of Computer Engineering and Computer Science, JB Speed Building, Louisville, KY 40292, USA
A fundamental problem in the human genome project is uncovering the correct assembly of the human genome. Many studies, including transcriptional analysis, SNP detection and characterization, gene finding and EST clustering, use genome assemblies as templates so it is important to determine the consistency among the various whole genome assemblies. A comparison of the order and orientation of the GenBank entries used to construct the NCBI and UCSC Goldenpath assemblies was made. In addition, a sequence level comparison was performed using MULTI, an efficient database search tool developed to make whole genome comparisons possible. The resulting comparisons show significant discrepancies in the sequence as well as in the order and orientation of GenBank entries used in constructing the NCBI and UCSC assemblies.