Mercurial > repos > iuc > meme_dreme
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 09:45:44 +0000 |
| parents | 3e5c80594237 |
| children | f33d77dcacce |
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<!DOCTYPE HTML> <html> <head> <meta charset="UTF-8"> <title>DREME</title> <script> // @JSON_VAR data var data = { "program": "dreme", "version": "5.0.5", "release": "Mon Mar 18 20:12:19 2019 -0700", "cmd": [ "dreme", "-o", "./dreme_out", "-p", "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink", "4", "-maxk", "10" ], "options": { "revcomp": false, "ngen": 100, "add_pv_thresh": 0.01, "seed": 1, "stop": { "evalue": "1e-05" } }, "alphabet": { "name": "RNA", "like": "rna", "ncore": 4, "symbols": [ { "symbol": "A", "name": "Adenine", "colour": "CC0000" }, { "symbol": "C", "name": "Cytosine", "colour": "0000CC" "symbol": "G", "name": "Guanine", "colour": "FFB300" "symbol": "U", "aliases": "T", "name": "Uracil", "colour": "008000" "symbol": "N", "aliases": "X.", "name": "Any base", "equals": "ACGU" "symbol": "V", "name": "Not U", "equals": "ACG" "symbol": "H", "name": "Not G", "equals": "ACU" "symbol": "D", "name": "Not C", "equals": "AGU" "symbol": "B", "name": "Not A", "equals": "CGU" "symbol": "M", "name": "Amino", "equals": "AC" "symbol": "R", "name": "Purine", "equals": "AG" "symbol": "W", "name": "Weak", "equals": "AU" "symbol": "S", "name": "Strong", "equals": "CG" "symbol": "Y", "name": "Pyrimidine", "equals": "CU" "symbol": "K", "name": "Keto", "equals": "GU" "background": { "freqs": [0.221, 0.245, 0.221, 0.312] "sequence_db": { "count": 1000 "control_db": { "name": "shuffled positive sequences", "from": "shuffled", "count": 1000, "freqs": [0.221, 0.245, 0.221, 0.312] "motifs": [ "db": 0, "id": "UUYUCY", "alt": "DREME-1", "len": 6, "nsites": 459, "evalue": "3.3e-013", "p": 387, "n": 210, "pvalue": "2.6e-018", "unerased_evalue": "3.3e-013", "pwm": [ [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 0.294118, 0.000000, 0.705882], [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 1.000000, 0.000000, 0.000000], [0.000000, 0.474946, 0.000000, 0.525054] "matches": [ "seq": "UUUUCC", "p": 147, "n": 75, "pvalue": "1.8e-007", "evalue": "2.2e-002" </script> var site_url = "http://meme-suite.org"; //====================================================================== // end RasterizedAlphabet //====================================================================== //====================================================================== // start LogoMetrics object //====================================================================== * Initialise and display the download popup. </style> </head> <body data-scrollpad="true"> <!-- --> <div id="grey_out_page" class="grey_background" style="display:none;"> The name of the motif uses the IUPAC codes for nucleotides which has a different letter to represent each of the 15 possible combinations. The name is itself a representation of the motif though the position weight matrix is not directly equivalent as it is generated from the sites found that matched the letters given in the name. <p>The logo of the motif.</p> <p>The logo of the reverse complement motif.</p> <p>The E-value is the enrichment p-value times the number of candidate motifs tested.</p> <p>The enrichment p-value is calculated using Fisher's Exact Test for enrichment of the motif in the positive sequences.</p> <p>Note that the counts used in Fisher's Exact Test are made after erasing sites that match previously found motifs.</p> <p>The E-value of the motif calculated without erasing the sites of previously found motifs.</p> <p>Show more information on the motif.</p> <p>Submit your motif to another MEME Suite program or download your motif.</p> <h5>Supported Programs</h5> <dt>Tomtom</dt> <dd>Tomtom is a tool for searching for similar known motifs. <dt>MAST</dt> <dd>MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs. <dt>FIMO</dt> <dd>FIMO is a tool for searching biological sequence databases for sequences that contain one or more known motifs. <dt>GOMo</dt> <dd>GOMo is a tool for identifying possible roles (Gene Ontology terms) for DNA binding motifs. <dt>SpaMo</dt> <dd>SpaMo is a tool for inferring possible transcription factor complexes by finding motifs with enriched spacings. <!-- Page starts here --> <h1>DREME</h1> <h2>Discriminative Regular Expression Motif Elicitation</h2> For further information on how to interpret these results please access To get a copy of the MEME software please access If you use DREME in your research please cite the following paper:<br /> Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011. </body> </html>