Bailey Timothy L, Boden Mikael, Buske Fabian A, Frith Martin, Grant Charles E, Clementi Luca, Ren Jingyuan, Li Wilfred W, Noble William S
Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20.
The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.
MEME Suite网络服务器提供了一个统一的门户，用于在线发现和分析代表DNA结合位点和蛋白质相互作用结构域等特征的序列基序。流行的MEME基序发现算法现在由GLAM2算法补充，该算法允许发现包含缺口的基序。三种序列扫描算法——MAST、FIMO和GLAM2SCAN——允许在众多DNA和蛋白质序列数据库中扫描由MEME和GLAM2发现的基序。转录因子基序（包括使用MEME发现的那些）可以使用基序数据库扫描算法TOMTOM与许多流行的基序数据库中的基序进行比较。转录因子基序可以通过使用基序-GO术语关联工具GOMO与基因本体（GO）术语关联来进一步分析其推定功能。MEME输出现在包含每个发现的基序的序列标识，以及用于方便地将基序提交给序列和基序数据库扫描算法（MAST、FIMO和TOMTOM）或GOMO进行进一步分析的按钮。GLAM2输出同样包含用于使用GLAM2SCAN进行进一步分析以及使用不同参数重新运行GLAM2的按钮。所有基于基序的工具现在都通过Opal作为网络服务实现。源代码、二进制文件和网络服务器可在http://meme.nbcr.net免费用于非商业用途。
