MARS and RNAcmap3:The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

作     者：Ke Chen Thomas Litfin Jaswinder Singh Jian Zhan Yaoqi Zhou 

作者机构：Institute of Systems and Physical BiologyShenzhen Bay LaboratoryShenzhen 518055China Peking University Shenzhen Graduate SchoolShenzhen 518055China University of Science and Technology of ChinaHefei 230026China Suzhou Institute for Advanced ResearchUniversity of Science and Technology of ChinaSuzhou 215123China Institute for GlycomicsGriffith UniversitySouthportQLD 4222Australia 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2024年第22卷第1期

页      面：143-150页

核心收录：

学科分类：0710[理学-生物学] 08[工学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：supported by grants from the National Key R&D Program of China(Grant No.2021YFF1200400) the Major Program of Shenzhen Bay Laboratory,China(Grant No.S201101001) the Shenzhen Science and Technology Innovation Program,China(Grant No.KQTD20170330155106581) the Griffith University Postgraduate Fellowship,Australia 

主　　题：RNA sequence database Homology search Secondary structure MARS RNAcmap3 

摘      要：sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology ***,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than *** new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art *** also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to *** results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on *** is accessible at https://***/omix/release/OMIX003037,and RNAcmap3 is accessible at http://***/download/.