"... In PAGE 3: ...oint Genome Institute (http://www.jgi.doe.gov). Preliminary sequence data for Mycobacterium tuberculosis CDC1551 (sequence assembly of September 7, 2002) was obtained Table 1. The number of contigs containing repetitive elements and a high G+C-content on either end was determined for the four sequence assemblies shown (see Table2 for details) Genome sequence assembly origin Total number of contigs in Total number of contigs used for Number of contig ends containing repeatsb Number of contigs ends with high G+C-contentb sequence assembly mappinga One Both %c One Both %c L.lactis (A) 210 131 34 12 35 6 1 5 M.... In PAGE 4: ...CBI genome database (http://www.ncbi.nlm.nih.gov/). RESULTS AND DISCUSSION Reference mappings are used to validate mapping results Four different prokaryotic genome sequence assemblies were mapped onto their isogenic genome sequences as a control test of the performance of Projector 2. For this purpose, similar template genome sequences were available for three of the four genome sequence assemblies ( Table2 ). The success of ordering contigs of an unfinished genome is highly dependent on the similarity of the template genome.... In PAGE 4: ... These examples clearly illustrate the necessity to perform gap-closing primer design on high-quality and non-repetitive DNA sequences. The prediction of successful gap-closure PCRs is accurate To estimate the number of successful gap-closing PCRs, we determined the number of gaps lt;15 kb ( Table2 ). Such a gap size should be straightforward to close by direct PCR.... In PAGE 5: ...lactis MG1363 contigs mapped onto the L.lactis IL1403 template is calculated at 93% ( Table2 ), which is in good agreement with the reported 94% of gap-closing PCR products obtained in our previous study (6). This result indic- ates that the method for estimating the number of successful gap-closure PCRs is accurate.... In PAGE 5: ... Primer pairs for these gaps were designed on flanking contig ends. Repeat-masking provides robust mapping results The estimated success percentages of the gap-closing PCRs of the isogenic reference mappings using repeat-masked sequences, are close to 100% for the four different assemblies, which indicates that the number of large gaps is relatively small in the four genome sequence assemblies ( Table2 and Figures 2 and 3). Mappings with repeat-masking on the non- isogenic templates yield slightly lower numbers of estimated successful gap-closing PCRs than the reference mappings (Table 2 and Figure 3).... In PAGE 5: ... Repeat-masking provides robust mapping results The estimated success percentages of the gap-closing PCRs of the isogenic reference mappings using repeat-masked sequences, are close to 100% for the four different assemblies, which indicates that the number of large gaps is relatively small in the four genome sequence assemblies (Table 2 and Figures 2 and 3). Mappings with repeat-masking on the non- isogenic templates yield slightly lower numbers of estimated successful gap-closing PCRs than the reference mappings ( Table2 and Figure 3). Without repeat-masking, a significant drop in the number of correctly mapped contigs and, thus, in successful gap-closing PCRs is observed for all assemblies (Table 2 and Figure 3).... In PAGE 5: ... Mappings with repeat-masking on the non- isogenic templates yield slightly lower numbers of estimated successful gap-closing PCRs than the reference mappings (Table 2 and Figure 3). Without repeat-masking, a significant drop in the number of correctly mapped contigs and, thus, in successful gap-closing PCRs is observed for all assemblies ( Table2 and Figure 3). For the non-isogenic mappings, the number of correctly mapped contigs is approximately the same for M.... In PAGE 5: ...umbers are shown for mapping in (D). A dot (C15) indicates an incorrectly mapped contig on that line. Figure 3. Results of the mapping procedures described in Table2 . The per- centage of mapped contigs is plotted for four bacterial genome assemblies mapped onto (non-) isogenic templates (for details see Table 2).... In PAGE 6: ...e. unfinished genomic sequences, mapping was performed for the template genomes listed in Table2 after they had been divided into 10 equally sized template fragments. Mapping is performed on each of these 10 template sequences separately, yielding 10 separate maps.... In PAGE 6: ... As relatively low numbers of template fragments were used, multiplex PCR is expected to be successful in closing the gaps between contigs bridging multiple fragments of a template genome. In case repeat- masked target sequences were mapped onto multiple repeat- masked template fragments, almost all of the contigs were identically ordered when compared with the reference map- ping ( Table2 and Figure 3). The number of correctly mapped contigs decreases considerably when the multiple templates were not repeat-masked.... In PAGE 6: ... For M.tuberculosis, more contigs were mapped (545 and 548, repectively; Table2 ) than the total number of contigs used for mapping (491; Table 1), because some contigs were mapped onto multiple fragments of the template genome. Mapping success depends on sequence similarity and colinearity between target and template genomes In a previous study, we showed that a correlation exists between sequence similarity and mapping success.... In PAGE 6: ...tuberculosis CDC1551 mapped onto M.leprae is at an acceptable 54% ( Table2 ), demonstrating that by using tem- plate genome with limited colinearity, over half of the gaps are closed with a single run of the Projector 2 software. Conclusions Projector 2 accurately positions contigs of an unfinished gen- ome sequence onto a genome of a related organism.... ..."

"... In PAGE 7: ...icroarray. Of these, 32.5% were wild type, 50.6% were heterozygous, and 12% were homozygous for the poly- morphism ( Table1 ). For NAT2*A803G, 80 of 83 (96.... In PAGE 7: ...ig. 1. Representative genotyping results for the NAT2*T341C poly- morphism. Table1 . Genotyping results for NAT2 polymorphisms in this study.... In PAGE 11: ...and negative serum samples were tested simultaneously in three commercial allergen-specific IgE assays, and correlation coefficients were calculated based on all 44 samples ( Table1 ). All of the comparisons produced correlation coefficients .... In PAGE 11: ...1 for cat dander, F13 for peanut, W1 for short ragweed, and D2 for dust mite (D. farinae). Negative samples are identified with an N after the hyphen. In positive samples, the number after the hyphen indicates the ASM score. Table1 . Correlationa between microarray assay and commercial clinical allergen-specific IgE assays.... In PAGE 15: ... These openings, called arrays, enable access to the aluminum oxide substrate. A set of 21mer oligonucleo- tides (Isogen) was synthesized ( Table1 ) and spotted in 325-pL droplets, containing 0.1 mmol/L of the oligonu- cleotide mixture, on the arrays with a Packard BioChip Arrayer (Meriden).... ..."

"... In PAGE 12: ...irst, the simulations of tracking multiple targets are presented in Figs. 4 and 5. Its initial conditions and maneuvering situations are shown in Tables 1 and 2 respectively. After using Monte Carlo fifty runs, we have the simulation results whose average track- ing errors are shown in Table3 . Moreover, the position and velocity errors are shown in Figs.... ..."

"... In PAGE 13: ...2, which is comparable to levels of black/white residential segregation. 18 The last two columns of Table4 report 1997 listening data, by format and Hispanic status, for markets with 1997 Hispanic listening data. Like blacks, Hispanics listen to different programming than non - Hispanics.... ..."