title: Comparative analysis of human genome assemblies reveals genome-level differences.
abstract: Previous comparative analysis has revealed a significant disparity between the predicted gene sets produced by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics. To determine whether the source of this discrepancy was due to underlying differences in the genomic sequences or different gene prediction methodologies, we analyzed both genome assemblies in parallel. Using the GENSCAN gene prediction algorithm, we generated predicted transcriptomes that could be directly compared. BLAST-based comparisons revealed a 20-30% difference between the transcriptomes. Further differences between the two genomes were revealed with protein domain PFAM analyses. These results suggest that fundamental differences between the two genome assemblies are likely responsible for a significant portion of the discrepancy between the transcript sets predicted by the two groups.
authors.affiliation: Tularik, Inc. Two Corporate Drive, South San Francisco, California 94080, USA.
authors.forename: Shuyu
authors.initials: S
authors.lastname: Li
authors.forename: Jiayu
authors.initials: J
authors.lastname: Liao
authors.forename: Gene
authors.initials: G
authors.lastname: Cutler
authors.forename: Timothy
authors.initials: T
authors.lastname: Hoey
authors.forename: John B
authors.initials: JB
authors.lastname: Hogenesch
authors.forename: Michael P
authors.initials: MP
authors.lastname: Cooke
authors.forename: Peter G
authors.initials: PG
authors.lastname: Schultz
authors.forename: Xuefeng Bruce
authors.initials: XB
authors.lastname: Ling
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D015894:Genome, Human; D006801:Humans; D008390:Markov Chains