Next generation transcriptomes for next generation genomes using est2assembly.
Next generation transcriptomes for next generation genomes using est2assembly.
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DOI：
10.1186/1471-2105-10-447
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发表时间：
2009-12-24
影响因子：
3
通讯作者：
Heckel DG
中科院分区：
文献类型：
--
作者：
Papanicolaou A;Stierli R;Ffrench-Constant RH;Heckel DG
基于毛细管的桑格测序和下一代技术（如454焦磷酸测序）的成本不断下降，促使非模式物种中的转录组项目激增，即使是转录组的浅层测序现在也可以用于检查一系列研究问题。数据的快速增长已经超过了研究非模式物种的研究人员有效分析和挖掘转录组数据的能力。在这里，我们提出了一个半自动化平台“est2assembly”，它将来自桑格或454测序的原始序列数据处理成混合从头组装，对其进行注释并产生GMOD兼容的输出，包括适合GBrowse的SeqFeature数据库。用户能够参数化装配变量，判断装配质量，并确定其特定需求的最佳装配。我们使用est2assembly来处理果蝇和Bicyclus的公开桑格EST数据，然后将它们与已发表的454个数据以及8个新的昆虫转录组集合进行比较。分析如此广泛的数据使我们能够了解这些新技术如何帮助EST项目设计。我们确定，汇编程序参数化是必不可少的标准化方法来判断ESTs项目的输出。此外，即使使用454的浅测序也产生足够的数据以广泛用于社区。est2assembly是一个重要的工具，以协助手动管理基因模型，一个重要的资源本身的权利，但特别是物种是由于获得基因组计划使用下一代测序。
The decreasing costs of capillary-based Sanger sequencing and next generation technologies, such as 454 pyrosequencing, have prompted an explosion of transcriptome projects in non-model species, where even shallow sequencing of transcriptomes can now be used to examine a range of research questions. This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently. Here we present a semi-automated platform 'est2assembly' that processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse. Users are able to parameterize assembler variables, judge assembly quality and determine the optimal assembly for their specific needs. We used est2assembly to process Drosophila and Bicyclus public Sanger EST data and then compared them to published 454 data as well as eight new insect transcriptome collections. Analysis of such a wide variety of data allows us to understand how these new technologies can assist EST project design. We determine that assembler parameterization is as essential as standardized methods to judge the output of ESTs projects. Further, even shallow sequencing using 454 produces sufficient data to be of wide use to the community. est2assembly is an important tool to assist manual curation for gene models, an important resource in their own right but especially for species which are due to acquire a genome project using Next Generation Sequencing.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
64.8
作者：
Brakefield, PM;Gates, J;Carroll, SB
通讯作者：
Carroll, SB
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
DOI：
10.1098/rstb.1998.0323
发表时间：
1998-10-29
期刊：
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES
影响因子：
--
作者：
Heckel, DG;Gahan, LJ;Trowell, S
通讯作者：
Trowell, S
影响因子：
5.8
作者：
Huntley, D;Baldo, A;Sergot, M
通讯作者：
Sergot, M