Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
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DOI：
10.1186/1471-2164-9-106
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发表时间：
2008-02-28
期刊：
影响因子：
4.4
通讯作者：
Odenwald WF
中科院分区：
文献类型：
--
作者：
Yavatkar AS;Lin Y;Ross J;Fann Y;Brody T;Odenwald WF
多基因组比较分析对基因调控的分子细节产生了重要的见解。我们已经开发了evopprinter，这是一个网络访问的基因组学工具，可以提供一个不间断的保守序列视图，因为它们出现在感兴趣的物种中。evopprint以接近碱基对的分辨率显示那些对基因功能至关重要的序列。EvoPrinterHD是第二代比较基因组学工具，可以自动从单个输入序列生成进化上遥远物种之间序列保守的增强视图。EvoPrinterHD目前可用于5种线虫、3种蚊子、12种果蝇、20种脊椎动物、17种葡萄球菌和20种肠道细菌的基因组，它采用了一种改进的BLAT算法[enhanced-BLAT (eBLAT)]，与早期EvoPrinter程序中使用的BLAT比对所识别的保守碱基相比，可检测到高达75%的保守碱基。新程序还可以识别重排DNA中的保守序列，突出重复DNA，并检测测序间隙。EvoPrinterHD目前在内存中拥有超过1120亿bp的索引基因组，并具有选择基因组子集进行分析的灵活性。还生成一个EvoDifferences配置文件来描绘在任何一个同源物中唯一丢失的保守序列。最后，EvoPrinterHD结合了以下选项：(1)使用不同的基因组比对区域作为参考DNA重新启动分析，以检测不太保守区域的物种特异性变化；(2)快速提取和管理保守序列；(3)对于细菌，识别基因组亚群中存在的独特或独特共享序列。EvoPrinterHD是一种快速、高分辨率的比较基因组学工具，可以自动生成不间断的以物种为中心的序列保守视图，并能够在重排的DNA中发现保守序列。当与cis-Decoder（一种发现组织特异性增强子之间共享的序列元素的程序）结合使用时，EvoPrinterHD有助于分析对协调基因调控至关重要的保守序列。
Multi-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We have developed EvoPrinter, a web-accessed genomics tool that provides a single uninterrupted view of conserved sequences as they appear in a species of interest. An EvoPrint reveals with near base-pair resolution those sequences that are essential for gene function. We describe here EvoPrinterHD, a 2nd-generation comparative genomics tool that automatically generates from a single input sequence an enhanced view of sequence conservation between evolutionarily distant species. Currently available for 5 nematode, 3 mosquito, 12 Drosophila, 20 vertebrate, 17 Staphylococcus and 20 enteric bacteria genomes, EvoPrinterHD employs a modified BLAT algorithm [enhanced-BLAT (eBLAT)], which detects up to 75% more conserved bases than identified by the BLAT alignments used in the earlier EvoPrinter program. The new program also identifies conserved sequences within rearranged DNA, highlights repetitive DNA, and detects sequencing gaps. EvoPrinterHD currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An EvoDifferences profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, EvoPrinterHD incorporates options that allow for (1) re-initiation of the analysis using a different genome's aligning region as the reference DNA to detect species-specific changes in less-conserved regions, (2) rapid extraction and curation of conserved sequences, and (3) for bacteria, identifies unique or uniquely shared sequences present in subsets of genomes. EvoPrinterHD is a fast, high-resolution comparative genomics tool that automatically generates an uninterrupted species-centric view of sequence conservation and enables the discovery of conserved sequences within rearranged DNA. When combined with cis-Decoder, a program that discovers sequence elements shared among tissue specific enhancers, EvoPrinterHD facilitates the analysis of conserved sequences that are essential for coordinate gene regulation.
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影响因子：
14.9
作者：
Lawson, Daniel;Arensburger, Peter;Atkinson, Peter;Besansky, Nora J;Bruggner, Robert V;Butler, Ryan;Campbell, Kathryn S;Christophides, George K;Christley, Scott;Dialynas, Emmanuel;Emmert, David;Hammond, Martin;Hill, Catherine A;Kennedy, Ryan C;Lobo, Neil F;MacCallum, M Robert;Madey, Greg;Megy, Karine;Redmond, Seth;Russo, Susan;Severson, David W;Stinson, Eric O;Topalis, Pantelis;Zdobnov, Evgeny M;Birney, Ewan;Gelbart, William M;Kafatos, Fotis C;Louis, Christos;Collins, Frank H
通讯作者：
Collins, Frank H
影响因子：
11.4
作者：
LI, XL;GUTJAHR, T;NOLL, M
通讯作者：
NOLL, M
影响因子：
4.6
作者：
Markstein, M;Zinzen, R;Levine, M
通讯作者：
Levine, M
影响因子：
5.8
作者：
Gallo, SM;Li, L;Halfon, MS
通讯作者：
Halfon, MS
影响因子：
2.7
作者：
Yuh, CH;Brown, CT;Davidson, EH
通讯作者：
Davidson, EH