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Palenik et al. 10.1073/pnas.0611046104. |
Fig. 4. GC content of chromosome 2 of O. tauri (A) and O. lucimarinus (B) genomes. Each point is the GC content (y axis) of the coding sequence of a single gene, the start position of which is shown on the x axis. The horizontal line is the average GC; the curved lines are spline fits to the data at several levels of smoothness. O. lucimarinus, Chr 2, average GC content: low, 48% (region 337,000-718,000 bp); high, 61%; all, 56%. O. tauri, Chr 2, average GC content: low, 51% (region 1-555,000 bp); high, 60%; all, 57%.
Fig. 5. Fractions of different functional types of DNA sequences of O. lucimarinus chromosomes conserved at the level of 70% sequence identity/100 bp or higher in O. tauri. Chromosome 18 shows significant deviation. This figure shows the level of similarity in the DNA sequence alignment of the two species obtained by VISTA (1). First, we obtained a map of large blocks of conserved synteny between the two species by applying Shuffle-LAGAN (2) global chaining algorithm to local alignments produced by translated BLAT (3). After that we applied Supermap, the fully symmetric whole-genome extension to the Shuffle-LAGAN algorithm (2). Then, in each syntenic block we applied Shuffle-LAGAN a second time to obtain a more fine-grained map of small-scale rearrangements such as inversions. We have also extended this approach to align duplicated segments in both genomes. Depending on the chromosome, from 50% to 70% of total exon length belongs to highly conserved intervals (above 70% nucleotide identity over 100 bp). Chromosome 18 in O. lucimarinus is an exception with only 15% of its total exon length located in conserved intervals.
1. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) Nucleic Acids Res 32:W273-W279.
2. Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S (2003) Bioinformatics 19S1:i54-i62
3. Kent WJ (2002) Genome Res 12:656-664
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