"... In PAGE 3: ...able 2: Current Status of Human Genome Sequencing Process (Jan 5, 2003)*.......17 Table3... ..."

"... In PAGE 6: ... Estimating the actual costs of human genomic sequencing is certainly hazardous. Nevertheless, our best effort is summarized in Table5 . Assuming op- timistically that clone-by-clone sequencing of hu- man DNA can be completed for $0.... ..."

"... In PAGE 6: ... Filling gaps and resolving uncertainties would add additional costs to whole-genome shotgun sequencing in the next century. We assert that the goals listed in Table1 are the true motivation for sequencing the human genome, not the accomplishment of some arbitrary, mythi- cal goal of 99.99% accuracy of a single, artifactual (in places) and nonrepresentative copy of the ge- nome.... ..."

"... In PAGE 6: ...8.73 clone coverage. The second data set was from the publicly funded Human Genome Project (PFP) and is primarily derived from BAC clones (30). The BAC data input to the assemblies came from a download of GenBank on 1 September 2000 ( Table2 ) totaling 4443.3 Mbp of sequence.... In PAGE 6: ...0 Mbp from the Phase 1 and 2 data, and 16.1 Mbp from the Phase 0 data ( Table2 ). This left us with a total of 4363.... ..."

"... In PAGE 3: ...able 1. Transition Probablities for CpG island prediction with HMM model..........16 Table2 : Current Status of Human Genome Sequencing Process (Jan 5, 2003)*.... ..."

"... In PAGE 4: ...not identified through homology modeling or in the structural genomics targets yet have significant presence in the human genome; and simple charts showing the distribution of the 5 genome sequences, PDB structures, structural genomics tar- gets or homology models. Most distributions are accompanied by two tables illustrating, first, the functional coverage by each data type ( Table1 ), and second, the correlation between input data types (data not shown). The actual overlap between these 10 groups will be added as part of an on-going development.... In PAGE 4: ... The actual overlap between these 10 groups will be added as part of an on-going development. For example in Table1 , PDB structures cover 37.2% of the iden- tified molecular functions in the human genome; if solved, structural genomics targets cover 32.... ..."

"... In PAGE 2: ... Current genome assemblies have several thousands of gaps, causing bad gene model predictions due to missing exons and splice sites. Statistics for the chicken and cow genomes compared with the human, mouse and rat genomes ( Table1 ) reveal fundamental problems in genomic structural and functional annota- tion in livestock genomes. Livestock genomes will always have low build numbers compared with model organisms such as human and mouse and yet they have comparable numbers of genes (UniGene).... In PAGE 5: ... While EBI-GOA uses an electronic mapping strategy to rapidly provide GO annotations for a large number of gene products, these are IEA mappings that rely on curated information from SwissProt, InterPro and the Enzyme Commission (EC) databases [16]. Many agricultural gene products are apos;predicted apos; products based on gene predic- tion algorithms ( Table1 ) and do not exist in these curated databases. However, GO annotation can be assigned based on human interpretation of sequence and/or struc- tural similarities (ISS) with well-studied and already GO- annotated gene products.... In PAGE 5: ... Our GO annotation strategy first provides breadth by focusing on the large proportion of gene products that currently exist in the UniParc database and have no GO annotation. Since predicted proteins represent approxi- mately half of the gene products from newly sequenced genomes ( Table1 .), being able to provide GO annota- tions for these gene products complements the GO anno- tations provided by EBI-GOA and dramatically improves Page 5 of 13 (page number not for citation purposes) with ESTs in the visualizations to address this shortcom- ing.... In PAGE 7: ... (1) Unlike EBI-GOA, AgBase does not currently annotate to IEA. (2) In newly sequenced genomes, such as cow and chicken, a large proportion of gene products are not represented in the UniProtKB database ( Table1 ) and are not annotated by EBI-GOA. To complement the EBI- GOA annotation effort and provide breadth of coverage, we identify the expression of these apos;predicted apos; gene products in vivo and, where possible, provide GO annotations.... ..."

"... In PAGE 3: ...671 contained at least 10 fragments ( Table1 ; for complete data see ftp://ftp.... In PAGE 4: ... In particular, repeat expansion produces numerous low-complexity periodic sequences (29). However, although consensuses of several of our 20 abundant classes are low- complexity, none of them are simple two- or three-nucleotide repeats ( Table1 ) which are the most typical microsatellites. Other abundant classes have no obvious features making them distinct at the DNA level and are probably common due to selection.... ..."