MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads.
MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads.
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MapNext：用于剪接和非剪接比对以及短序列读取的 SNP 检测的软件工具
DOI：
10.1186/1471-2164-10-s3-s13
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发表时间：
2009-12-03
期刊：
影响因子：
4.4
通讯作者：
Shi S
中科院分区：
文献类型：
--
作者：
Bao H;Xiong Y;Guo H;Zhou R;Lu X;Yang Z;Zhong Y;Shi S
背景下一代测序技术为转录组学和群体基因组学的研究提供了令人兴奋的途径。有一个越来越多的需要进行剪接和未剪接的短转录读到一个参考基因组和估计次要等位基因频率从序列的人口samples.ResultsWe设计和实施MapNext，一个软件工具，剪接和未剪接的短序列读到参考序列的比对，和自动SNP检测使用邻域质量标准。MapNext提供了四种主要分析：（i）未剪接比对和读数聚类，（ii）转录本读数在内含子边界上的剪接比对，（iii）SNP检测和估计来自群体序列的次要等位基因频率，以及（iv）将结果数据存储在数据库中，以使其可用于更灵活的查询和进一步分析。该软件工具已被测试使用模拟和真实的data.ConclusionMapNext是一个全面的和强大的工具，剪接和未剪接的短读段和自动SNP检测从人口序列的比对。MapNext的简单性，灵活性和效率使其成为转录组学和群体基因组学研究的宝贵工具。
BackgroundNext-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples.ResultsWe have designed and implemented MapNext, a software tool for both spliced and unspliced alignments of short sequence reads onto reference sequences, and automated SNP detection using neighbourhood quality standards. MapNext provides four main analyses: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcript reads over intron boundaries, (iii) SNP detection and estimation of minor allele frequency from population sequences, and (iv) storage of result data in a database to make it available for more flexible queries and for further analyses. The software tool has been tested using both simulated and real data.ConclusionMapNext is a comprehensive and powerful tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences. The simplicity, flexibility and efficiency of MapNext makes it a valuable tool for transcriptomic and population genomic research.