Genetic Causes of Disease Group, Genes and Disease Program, Centre for Genomic Regulation, Pompeu Fabra University, Barcelona, Catalonia, Spain.
Nucleic Acids Res. 2010 Mar;38(5):e34. doi: 10.1093/nar/gkp1127. Epub 2009 Dec 11.
High-throughput sequencing technologies enable direct approaches to catalog and analyze snapshots of the total small RNA content of living cells. Characterization of high-throughput sequencing data requires bioinformatic tools offering a wide perspective of the small RNA transcriptome. Here we present SeqBuster, a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets. The high flexibility of this tool is illustrated by the multiple choices offered in the pre-analysis for mapping purposes and in the different analysis modules for data manipulation. To overcome the storage capacity limitations of the web-based tool, SeqBuster offers a stand-alone version that permits the annotation against any custom database. SeqBuster integrates multiple analyses modules in a unique platform and constitutes the first bioinformatic tool offering a deep characterization of miRNA variants (isomiRs). The application of SeqBuster to small-RNA datasets of human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some of them being associated to stem cell differentiation. The exhaustive description of the isomiRs provided by SeqBuster could help to identify miRNA-variants that are relevant in physiological and pathological processes. SeqBuster is available at http://estivill_lab.crg.es/seqbuster.
高通量测序技术使人们能够直接对活细胞中总小 RNA 含量的瞬时样本进行编目和分析。高通量测序数据的特征需要提供小 RNA 转录组广泛视角的生物信息学工具。在这里，我们展示了 SeqBuster，这是一个功能强大且可靠的基于网络的工具包，可用于处理和分析大规模小 RNA 数据集。该工具的高灵活性通过在映射目的的预分析中提供的多种选择以及在用于数据操作的不同分析模块中得到体现。为了克服基于网络的工具的存储容量限制，SeqBuster 提供了一个独立版本，允许针对任何自定义数据库进行注释。SeqBuster 将多个分析模块集成到一个独特的平台中，是第一个提供 miRNA 变体（isomiRs）深度特征分析的生物信息学工具。SeqBuster 在人类胚胎干细胞小 RNA 数据集上的应用表明，大多数 miRNA 呈现不同类型的 isomiRs，其中一些与干细胞分化有关。SeqBuster 提供的 isomiRs 的详尽描述可以帮助识别在生理和病理过程中相关的 miRNA 变体。SeqBuster 可在 http://estivill_lab.crg.es/seqbuster 上获取。
