SpBase: A Database System For Echinoderm Genome Information

描述(申请人提供)：这个项目的总体目标是通过一个易于管理的网络信息系统(http://spbase.org).)收集、整理和呈现棘皮动物物种的基因组信息，包括参考的紫球棘皮动物(Sp)这些努力的直接重点是向实验室科学家提供关于基因组序列、基因结构、表达数据和功能信息的最新信息，以促进实验研究发育中的基因调控。最初的参考序列草案由贝勒医学院人类基因组测序中心(BCM-HGSC)承担，并于2006年发表(海胆基因组测序联盟，2006年)。今天，这一领域的努力既有 鉴于大量关于参考物种和相关物种的新出现的序列信息，具有挑战性和趣味性。一组全新的Sp基因组已经提交给Genbank，等待SpBase的进一步注释。然而，初步测量表明，这个版本要完整得多，它可以揭示以前无法获得的基因组组织的科学有趣元素。许多物种的单个实验室转录组测序项目正在以极快的速度出现。这些数据集很少被分析过最初进行实验的问题，但它们可以提供关于基因结构的全基因组信息，如组织特异性剪接异构体。为了支持BCM-HGSC，我们还为其他基因组测序项目提供了材料，这些项目包括巴西球藻、弗朗西斯坎氏球藻、杂色石斑鱼、刺五加真核生物和微小拟小球藻。所有这些物种的新序列数据已经获得，在某些情况下已经发布到Genbank上。只要仔细管理和张贴，这些材料将丰富SpBase的产品。

DESCRIPTION (provided by applicant): The overall aim of this project is to gather, collate and present genomic information for echinoderm species including the reference, Strongylocentrotus purpuratus (Sp) through an easily managed web information system (http://spbase.org). These efforts are directly focused to provide the bench scientist with up to date information on the genome sequence, gene structures, expression data and functional information in order to facilitate experiments to study gene regulation in development. Originally a draft sequence for the reference was undertaken by the Baylor College of Medicine, Human Genome Sequencing Center (BCM-HGSC) and published in 2006 (Sea Urchin Genome Sequencing Consortium, 2006). Today efforts in this area are both challenging and interesting in view of the large body of emerging sequence information on the reference and allied species. An entirely new assembly of the Sp genome has been submitted to Genbank and awaits further annotation at SpBase. However, preliminary measurements indicate that this version is so much more complete that it can reveal scientifically interesting elements of genome organization that were unattainable previously. Individual laboratory transcriptome sequencing projects for many species are appearing at a great rate. These datasets are seldom analyzed past the experimental question for which they were originally conducted, yet they can provide genome wide information on gene structure such as tissue specific splicing isoforms. In support of the BCM-HGSC, we have provided material for additional genome sequencing projects including Allocentrotus fragllis, S. franciscanus, Lytechinus variegatus, Eucidaris tribuloides and Patiria miniata. New sequence data for all of these species has been procured and in some cases already posted to Genbank. This is the material that will enrich the offering of SpBase provided it is carefully managed and posted.