在大多数真核生物中,小RNA(sRNA)分子,如miRNA,siRNA和piRNA调节基因表达并抑制转座子和病毒。AGO/PIWI家族蛋白根据大小对功能sRNA进行排序,5'-核苷酸和其他序列特征。在植物和一些动物中,病毒sRNAs极其多样,覆盖整个病毒基因组序列,通过病毒sRNA的深度测序和生物信息学分析,可以从头重建完整的病毒基因组。以前,我们已经开发了一个工具MISIS来查看和分析病毒和细胞基因组区域的sRNA图谱,产生多个sRNA。在这里,我们描述了MISIS的新版本,MISIS-2,它能够确定和可视化共有序列,并对任何选定大小和5'末端核苷酸身份的sRNA进行计数。此外,我们证明了MISIS-2用于鉴定参考序列每个位置的单核苷酸多态性(SNP)以及在进化的病毒准种中重建共有主基因组的实用性。MISIS-2是一个Java独立的程序。它与源代码一起在网站http://www上免费提供。fasteris.com/apps.
In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5\'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a
consensus sequence and count sRNAs of any chosen sizes and 5\'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a
consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps.