MEME Suite: tools for motif discovery and searching
Citations
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Cites background from "MEME Suite: tools for motif discove..."
...Received on December 17, 2010; revised on January 26, 2011; accepted on February 1, 2011...
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Cites methods from "MEME Suite: tools for motif discove..."
...Six of these tools––DREME (3), MEME-ChIP (4), CentriMo (6), AME (7), SpaMo (8) and MCAST (12)––were developed or given web interfaces since the last publication describing the MEME Suite (15)....
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...Tools added since the MEME Suite web server was last described (15) are underlined....
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1,967 citations
References
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"MEME Suite: tools for motif discove..." refers methods in this paper
...The MEME algorithm (2) has been widely used for the discovery of DNA and protein sequence motifs, and MEME continues to be the starting point for most analyses using the MEME Suite....
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...MEME (2) and GLAM2 (3) are tools for motif discovery, TOMTOM (4) searches for similar motifs in databases of known motifs, FIMO, GLAM2SCAN (3) and MAST (5) search for occurrences of motifs in sequence databases, and GOMO (6) provides associations between motifs and GO terms....
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2,216 citations
"MEME Suite: tools for motif discove..." refers background in this paper
...It offers a significantly expanded set of programs for these tasks compared with the earlier web server (1)....
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"MEME Suite: tools for motif discove..." refers background or methods in this paper
...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....
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...This type of analysis is done using TOMTOM....
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...MEME (2) and GLAM2 (3) are tools for motif discovery, TOMTOM (4) searches for similar motifs in databases of known motifs, FIMO, GLAM2SCAN (3) and MAST (5) search for occurrences of motifs in sequence databases, and GOMO (6) provides associations between motifs and GO terms....
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...TOMTOM not only provides a numeric score for the match between two motifs, but also provides an estimate of the statistical significance of the score....
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...TOMTOM (4) quantifies the similarity between two motifs, and can be used to search a database of known motifs for matches to motifs found by MEME....
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