Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-1

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>nces of soybean DNA, and estimation of copy number. Copy number was estimated according to the number of sequence survey reads aligning to each 1 kb window of the BACs. The alignment represents the superposition of identical or closely related sequences on the BAC sequence, in order to visualize the individual reads showing regions present in many copies per genome. The BAC sequences were: A) The euchromatic BAC described by Clough .(20); B) the euchromatic BAC GM_WBb0098N11; C) the BAC GM_WBb0078A23 from a heterochromatic regio

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-0

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>abases and the top significant (1E-6) hit recorded. Percentages represent the percentage of reads with hits to sequences from a particular organism with respect to all reads with hits to the TIGR repeats. B) Distribution of hits to plant repeat databases, by class of repetitive element Raw reads from the genomic sequence survey were matched to the combined plant repeat databases as for (A), and the class of repetitive element for the top hit was used to show the relative abundance of different classes of repetitive elements. This gives an estimate of the relative frequency of these families in the soybean genome. Retrotransposons and rDNA are the most common classes of repeat. See Additional File for common repeat sequences not included in the TIGR database

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-2

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>T with e < 1E-6). The total number of sequences matching at 95% or higher identity is 37% of total EST clones. Note that few sequences match at 100% identity due to the error rate of the 454 pyrosequencing used for this study.B) Coding fragments discovered within the short reads (with e values to the GenBank protein (nr) database < 1E-6), and their closest protein-level sequence hit by taxonomy of the source organism of the database sequence