Wang Hao, McManus Joel, Kingsford Carl
Computational Biology Department, School of Computer Science and.
Computational Biology Department, School of Computer Science and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085. Epub 2016 Feb 15.
: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping.
Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap
Supplementary data are available at Bioinformatics online.
核糖体谱分析是一种最近开发的高通量测序技术，它在翻译过程中捕获长度约为30bp的核糖体保护的mRNA片段。由于可变剪接和重复序列，一个核糖体保护的读段可能会映射到转录组中的多个位置，使用标准方法时会导致丢弃或任意映射。我们提出了一种技术和软件，通过将读段按估计的转录本丰度比例分配到潜在来源来解决这个问题。与简单映射相比，这能更准确地估计核糖体谱。
Ribomap可在http://www.cs.cmu.edu/∼ckingsf/software/ribomap上作为开源软件获取。
补充数据可在《生物信息学》在线获取。
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