Six sequencing methods with more than 5 projects. doi:10.1371/journal.pone.0048837.gMethods Mapping of draft contigs to a finished genomeComparisons between the finished and draft versions of each AVP site genome were performed using the NUCmer pipeline (part of MUMmer [17]) with no options, using the finished sequence as the `reference’ and the draft sequence as the `query.’ The alignments were mapped to the finished genome and each aligned base position designated as `mapped.’ These alignments provided the number of covered bases in the finished genome and the locations of gaps, i.e., regions missing from the draft contigs.Characterization of gapsTo characterize the content missing in the draft contigs, Prodigal [8] (v2.5) was used to predict protein coding genes on the draft contigs. Proteins encoded in the finished genome were then compared with those predicted in the draft genome using NCBI BLASTp [18]. Each protein in the finished genome was assigned to one of the following groups: identical proteins in both versions; similar full- length proteins (e.g., a sequence correction); longer in the draft and 100 identical (e.g., likely a frameshift); low quality hits (e.g., probably not in the draft), and proteins that had no hit. To determine if the missing protein coding genes (belonging to the last two groups) were actually present in the draft sequence butFigure 6. Distributions of functions, based on COG group assignments, of gene sequences missing in draft assemblies. Data is shown for six sequencing technologies; omitted is Illumina PacBio for which there are currently only eight genome projects without any missing genes. doi:10.1371/journal.pone.0048837.gDraft vs Finished GenomesTable 2. Correlation of the number of contigs with genome GC , repeat content, and size.Technology Sanger Sanger, 454-FLX 454-Ti, 454-Ti-PE 454-Ti, 454-Ti-PE, Illumina Std(PE) Illumina Std(PE) Illumina Std(PE)LMP(I) Illumina Std(PE)LMP(II) Illumina Std(PE)LMP+PacBio Data shown are the Kendall rank correlation coefficients. * = pvalue,0.05. doi:10.1371/journal.pone.0048837.tGC 0.091 0.017 0.032 0.168 0.255 0.047 20.370 20.Short Tubastatin A custom synthesis repeats 0.356 * 0.372 * 0.525 * 0.276 0.373 * 0.647 * 0.540 0.749 *Medium repeats 0.277 * 0.355 * 0.721 * 0.295 0.342 0.44 * 0.89 * 0.Long repeats 0.170 0.224 * 0.579 * 0.295 0.135 0.481 * 0.167 0.Genome size 0.356 * 0.278 * 0.249 0.360 0.556 * 0.485 * 0.077 0.had not been predicted by Prodigal, tBLASTn was used to search for those genes in the draft contigs.Supporting InformationTable S1 List of genomes and their features used for this study. (XLS)Identification of repeatsA repeat content `profile’ was generated for each genome that included both the repeat lengths (bp) and the number of occurrences 23977191 for each. Megablast was run on each genome against itself. Then the RECON tool [19] was used to group the repeats into families and to screen for repeats that are at least 50 bases long and 95 identical to each other.Author ContributionsConceived and designed the experiments: KM NK TW RC HK. Performed the experiments: KM ML AC AC AL. Analyzed the data: KM A. Clum ML. Contributed reagents/materials/analysis tools: DQ TB ML A. Copeland LG. Wrote the paper: KM.
Pluripotent embryionic stem cells (ESC) derived from the inner mass of the pre-implanted embryos have the ability to self-renew indefinitely in vitro and in appropriate conditions can be enforced to differentiate into a diversity of specialized cell types. Recently, it has been shown tha.Six sequencing methods with more than 5 projects. doi:10.1371/journal.pone.0048837.gMethods Mapping of draft contigs to a finished genomeComparisons between the finished and draft versions of each genome were performed using the NUCmer pipeline (part of MUMmer [17]) with no options, using the finished sequence as the `reference’ and the draft sequence as the `query.’ The alignments were mapped to the finished genome and each aligned base position designated as `mapped.’ These alignments provided the number of covered bases in the finished genome and the locations of gaps, i.e., regions missing from the draft contigs.Characterization of gapsTo characterize the content missing in the draft contigs, Prodigal [8] (v2.5) was used to predict protein coding genes on the draft contigs. Proteins encoded in the finished genome were then compared with those predicted in the draft genome using NCBI BLASTp [18]. Each protein in the finished genome was assigned to one of the following groups: identical proteins in both versions; similar full- length proteins (e.g., a sequence correction); longer in the draft and 100 identical (e.g., likely a frameshift); low quality hits (e.g., probably not in the draft), and proteins that had no hit. To determine if the missing protein coding genes (belonging to the last two groups) were actually present in the draft sequence butFigure 6. Distributions of functions, based on COG group assignments, of gene sequences missing in draft assemblies. Data is shown for six sequencing technologies; omitted is Illumina PacBio for which there are currently only eight genome projects without any missing genes. doi:10.1371/journal.pone.0048837.gDraft vs Finished GenomesTable 2. Correlation of the number of contigs with genome GC , repeat content, and size.Technology Sanger Sanger, 454-FLX 454-Ti, 454-Ti-PE 454-Ti, 454-Ti-PE, Illumina Std(PE) Illumina Std(PE) Illumina Std(PE)LMP(I) Illumina Std(PE)LMP(II) Illumina Std(PE)LMP+PacBio Data shown are the Kendall rank correlation coefficients. * = pvalue,0.05. doi:10.1371/journal.pone.0048837.tGC 0.091 0.017 0.032 0.168 0.255 0.047 20.370 20.Short repeats 0.356 * 0.372 * 0.525 * 0.276 0.373 * 0.647 * 0.540 0.749 *Medium repeats 0.277 * 0.355 * 0.721 * 0.295 0.342 0.44 * 0.89 * 0.Long repeats 0.170 0.224 * 0.579 * 0.295 0.135 0.481 * 0.167 0.Genome size 0.356 * 0.278 * 0.249 0.360 0.556 * 0.485 * 0.077 0.had not been predicted by Prodigal, tBLASTn was used to search for those genes in the draft contigs.Supporting InformationTable S1 List of genomes and their features used for this study. (XLS)Identification of repeatsA repeat content `profile’ was generated for each genome that included both the repeat lengths (bp) and the number of occurrences 23977191 for each. Megablast was run on each genome against itself. Then the RECON tool [19] was used to group the repeats into families and to screen for repeats that are at least 50 bases long and 95 identical to each other.Author ContributionsConceived and designed the experiments: KM NK TW RC HK. Performed the experiments: KM ML AC AC AL. Analyzed the data: KM A. Clum ML. Contributed reagents/materials/analysis tools: DQ TB ML A. Copeland LG. Wrote the paper: KM.
Pluripotent embryionic stem cells (ESC) derived from the inner mass of the pre-implanted embryos have the ability to self-renew indefinitely in vitro and in appropriate conditions can be enforced to differentiate into a diversity of specialized cell types. Recently, it has been shown tha.
