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Table 3. Comparison of two simple tiling metrics that incorporate repetitive nucleotides to improve non-repetitive sequence coverage. In Case 1, repeat sequences less than or equal to 50bp were allowed, and in Case 2 up to 25% of a tile may contain repetitive nucleotides. As in Table 1, tile sizes range from 300bp to 1.5kb. Case 1 achieves only marginal improvement in non-repetitive sequence coverage when compared with the same level of repeat nucleotide inclusion in the optimal tiling case. Non-repetitive sequence coverage in mammalian genomes falls sharply in Case 2 despite the inclusion of a high percentage of repetitive DNA. In each case, performance on mammalian genomes is significantly lower than that of the optimal tiling algorithm (Table 2).
2006
"... In PAGE 13: ... The linear-time tiling method was then applied to the sequences to derive an optimal tile path for each. Table3 includes a summary of two additional metrics that apply simple tiling schemes to each sequence. Each of the latter methods allows some inclusion of repetitive nucleotides in order to recover a higher percentage of non- repetitive DNA.... ..."
Cited by 3
Table 2: Genomic islands in the genome of Bacillus subtilis.
2004
"... In PAGE 4: ... subtilis has been assessed using a system of hidden Markov models in order to detect heterogenei- ties in DNA composition [24]. Table2 is an extended version summing up these findings and the location of CA clusters identified with the MPW approach. The table demonstrates that both algorithms identify with similar efficiency regions of deviating DNA composition.... ..."
Table 1. Genome coverage
2005
"... 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.... ..."
Table 1: Genome data
2007
"... In PAGE 2: ... In contrast, Saccharomy- cotina specific protein clusters are enriched in transcrip- tion and mitochondrion related functions. Results Overview of clustering results To compare the ORF content of Pezizomycotina and Sac- charomycotina we selected a set of 33 species shown in Table1 . 14 of them are Pezizomycotina and 13 Saccharo- mycotina.... In PAGE 4: ...1, as a good compromise between sensitivity and spe- cificity. We used the program InterProScan [23] to detect if pro- teins from a sub set of genomes ( Table1 ) had a sequence feature corresponding to an InterPro entry. InterPro is a database of known protein sequence features such as domains, families and active sites, i.... In PAGE 7: ... The dendrogram from hierarchical clustering is shown for columns and the phylum of species is indicated by a column colour bar between the heatmap and the dendrogram. Under the heatmap each spe- cies is specified by an abbreviation explained in Table1 . On the left side of the main heatmap a black and white side heatmap shows the percentage of ORFs in a cluster that have an InterPro entry of all cluster apos;s ORFs analysed with InterProScan ( quot;wIPR quot;), cluster apos;s stability and cluster apos;s Saccharomycotina to Pezizomycotina ratio in a clustering where inflation value (r) was 1.... In PAGE 14: ... Posi- tions of species analysed with InterProScan on the two PCs that explain the largest amount of variation in the counts of ORFs with an InterPro entry. Species abbreviations are explained in Table1 and data points are coloured by phyla. Page 14 of 23 (page number not for citation purposes) three times more ORFs with IPR001138 than a Saccharo-... In PAGE 16: ... The dendrogram from hierar- chical clustering is shown for columns and the phylum of spe- cies is indicated by a column colour bar between the heatmap and the dendrogram. Under the heatmap each spe- cies is specified by an abbreviation explained in Table1 . Left side heatmap shows the loading of the entry as in Figure 8a.... In PAGE 18: ...e. InterPro entries) with the program InterProScan from a subset of genomes in our data set ( Table1 ), counted ORFs having an entry and analysed the counts with PCA. The function of the 100 InterPro entries with most differ- ences between the species analysed (TOP 100) was stud- ied in detail.... In PAGE 19: ... Final data analysis and visualisation of results was done with custom R scripts using the Bioconductor libraries [49] when pos- sible. Retrieval and analysis of sequence data Protein sequences of predicted open reading frames (ORF), in fasta format, were retrieved from various sequencing centres as indicated in Table1 . They have been published in the following articles: S.... In PAGE 20: ... To find functional and pathway annotations for proteins Funcat [17-19] annotations were downloaded from MIPS [58] for genomes indicated in Table 1. Proteins from a subset of genomes ( Table1 ) were ana- lysed with InterProScan [16] to find features from their sequence, i.... In PAGE 20: ... InterPro entries found in the ORFs are provided [see additional file 4]. Proteins from a subset of genomes ( Table1 ) were ana- lysed also with Protfun [60] to predict their function and localisation. Protfun categories of proteins are provided [see additional file 5].... ..."
Table 3 Genomes and abbreviations used.
"... In PAGE 13: ... Statistical analyses and structure prediction approaches built upon the contents of the PDB need to take these biases into account so that they can be more readily applied to the emerging genome sequence data. Materials and methods A relational database of genome sequences and structure assignments Translated genome sequences were taken from the relevant web sites ( Table3 ). The genome data are constantly changing and are contingent on the current state of the art in gene finding.... ..."
Table 5. Costs of Human Genomic
1997
"... 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.... ..."
Cited by 21
Table 6: Limitations on the genome to be constructed
"... In PAGE 7: ... Table 5 shows the corresponding construction space and time for each genome. To conclude this section, Table6 shows the limitations on the index that can be constructed in an ordinary PC nowadays, assuming a RAM of size 4 Gbytes.6 5 Concluding Remarks We have demonstrated that CSA and FM-index can be constructed for a genome of length up to a few Gigabases.... ..."
Table 1. Genomic Variation Repositories
"... In PAGE 3: ... For example, aberrant promoter methylation associated with transcriptional downregulation of tumor suppressor genes has been found in basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (SCC), melanoma, and cutaneous lymphoma [8]. Though not exhaustive, Table1 gives a list of publicly available cancer-relevant large genomic variation repositories. Several projects attempt to comprehensively study genomic variation in cancer.... ..."
Table 1 Archaeal genomic data
"... In PAGE 2: ... Our results suggest archaea may have gene-regulation patterns other than those typical of eubacteria or eukaryotes. Materials and methods Genomes Genomic sequences of four archaea ( Table1 ) and their associated protein annotation tables were downloaded from GenBank, NCBI (http://www.... ..."
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