VmatchNL - a user-friendly graphical interface for large-scale genome analysis

描述（由申请人提供）：参考人类基因组序列的可用性为研究人类健康和疾病的遗传和分子基础提供了基础。使用各种现代技术来研究差异基因表达，学术和工业环境中的大量研究人员寻找特定基因和基因产物的激活或抑制对疾病的发作和进展的因果作用。生物信息学和计算方法在这些研究中发挥着关键作用。NewLink Genetics Corporation是一家生物制药公司，主要致力于开发新型药物和功能基因组学解决方案，主要关注癌症。该公司拥有自己的专有技术用于靶基因发现。为了促进其内部生物信息学分析，NewLink从爱荷华州州立大学获得了基因结构预测软件的许可，并从德国汉堡大学Stefan Kurtz教授获得了基因组规模序列匹配软件（“Vmatch”）的许可。这些程序是NewLink内部目标发现生物信息学管道的关键组成部分。Vmatch是一个基于增强后缀数组的多功能字符串匹配应用程序。认识到有数百家其他公司有类似的生物信息学需求，NewLink获得了Vmatch的独家分销和开发权，现在将该程序授权给营利性客户（该程序的学术版本仍然免费提供给非营利研究人员）。这项SBIR提案寻求资金开发VmatchNL，这是Vmatch软件的GUI驱动应用程序。我们业务的总体目标是将所有软件集成到一个GUI驱动的、行业质量的、用于靶基因发现的综合平台（“TargetSeqerNL”）中。这些产品的市场包括其他没有资源在内部开发类似功能的小公司，寻找GeneSeqer和Vmatch相对于其他程序的上级性能的大公司，以及有类似需求的学术研究人员组织和分析他们的基因表达数据。

DESCRIPTION (provided by applicant): The availability of a reference human genome sequence provides the foundation for studying the genetic and molecular basis of human health and disease. Using a variety of modern technologies to study differential gene expression, large numbers of researchers in both academic and industrial settings look for causative effects of activation or repression of particular genes and gene products with respect to the onset and progression of disease. Bioinformatic and computational approaches play a critical role in such studies. NewLink Genetics Corporation is a biopharmaceutical company developing novel drugs and functional genomics solutions with a primary focus on cancer. The company has its own proprietary technology for target gene discovery. To facilitate its in-house bioinformatic analysis, NewLink has licensed software for gene structure prediction from Iowa State University and software for genome-scale sequence matching ("Vmatch") from Prof. Stefan Kurtz, University of Hamburg, Germany. These programs are key components of NewLink's internal target-discovery bioinformatics pipeline. Vmatch is a versatile string matching application based on enhanced suffix arrays. Recognizing that there are hundreds of other companies with similar bioinformatics needs, NewLink acquired the exclusive distribution and development rights to Vmatch and is now licensing this program to for-profit customers (an academic version of the programs remains freely available to non-profit researchers). This SBIR proposal seeks funds to develop VmatchNL, a GUI driven application of the Vmatch software. The overall goals of our business are to integrate all software into a GUI-driven, industry-quality, comprehensive platform for target gene discovery ("TargetSeqerNL"). The market for these products includes other small companies that do not have the resources to develop similar capabilities in-house, big companies that look for the superior performance of GeneSeqer and Vmatch relative to other programs, and also to academic researchers with similar needs to organize and analyze their gene expression data.