Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7. doi: 10.1093/nar/gks1007. Epub 2012 Oct 30.
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue of 'building blocks' for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.
MODOMICS 是一个 RNA 修饰数据库，提供了有关修饰核苷酸碱基结构、生物合成途径、RNA 修饰酶以及 RNA 序列中修饰残基位置的综合信息。在当前可访问的数据库版本（http://modomics.genesilico.pl）中，我们包括了新的功能：人类和酵母 snoRNA 参与 RNA 指导的 RNA 修饰的普查、涵盖 5'端加帽过程的新部分，以及用于化学合成各种修饰核苷的“构建块”目录。RNA 修饰、RNA 修饰酶和修饰 RNA 的 MODOMICS 集合也已更新。添加了许多新鉴定的修饰核苷酸碱基和来自各种生物体的一百多种功能和结构特征明确的蛋白质。在 RNA 序列部分，添加了具有实验映射修饰核苷酸碱基的 snRNA 和 snoRNA，并大大扩展了当前的 rRNA 和 tRNA 序列集合。为了方便文献搜索，MODOMICS 中的每个记录都与其他数据库和选定的关键出版物进行了交叉引用。还实现了数据库搜索和查询的新选项，包括蛋白质序列的 BLAST 搜索和收集的核酸序列的 PARALIGN 搜索。
