MEME SUITE: tools for motif discovery and searching
| Autor: | William Stafford Noble, Jingyuan Ren, Luca Clementi, Fabian A. Buske, Martin C. Frith, Wilfred W. Li, Mikael Bodén, Timothy L. Bailey, Charles E. Grant |
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| Rok vydání: | 2009 |
| Předmět: |
0106 biological sciences
Web server Sequence analysis Computational biology Biology computer.software_genre Bioinformatics 01 natural sciences 03 medical and health sciences Protein sequencing MEME suite Sequence Analysis Protein Databases Genetic Genetics Regulatory Elements Transcriptional 030304 developmental biology Internet 0303 health sciences Binding Sites Sequence Analysis DNA Articles DNA binding site Multiple EM for Motif Elicitation Web service Sequence motif computer Algorithms Software Transcription Factors 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkp335 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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