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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e6639e130c5bf50f489dd09e38a1cbc712280fff
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 15:02:25 +0000 |
| parents | 7c5da353e460 |
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<HTML><HEAD><TITLE>.// - Homer de novo Motif Results</TITLE></HEAD> <BODY> <H1>Homer <i>de novo</i> Motif Results (.//)</H1> <A HREF="knownResults.html">Known Motif Enrichment Results</A><BR/> <A HREF="geneOntology.html">Gene Ontology Enrichment Results</A><BR/> If Homer is having trouble matching a motif to a known motif, try copy/pasting the matrix file into <A HREF="http://www.benoslab.pitt.edu/stamp/">STAMP</A><BR/> More information on motif finding results: <A HREF="http://biowhat.ucsd.edu/homer/">HOMER</A> | <A HREF="http://biowhat.ucsd.edu/homer/motif/index.html">Description of Results</A> | <A HREF="http://biowhat.ucsd.edu/homer/motif/practicalTips.html">Tips</A> <BR/> Total target sequences = 15<BR/> Total background sequences = 68<BR/> <FONT color="red">* - possible false positive</FONT><BR/> <TABLE border="1" cellpading="0" cellspacing="0"> <TR><TD>Rank</TD><TD>Motif</TD><TD>P-value</TD><TD>log P-pvalue</TD><TD>% of Targets</TD><TD>% of Background</TD> <TD>STD(Bg STD)</TD> <TD>Best Match/Details</TD><TD>Motif File</TD></TR> <TR><TD>1 <FONT color="red">*</FONT></TD><TD><svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,0,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,0,48.95)">G</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.271,2,48.9)">A</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.727,1,35.35)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.223,25,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.775,26,37.75)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,52,49)">A</text> <text fill="#0000EE" x="0" y="0" 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<text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.003,277,49)">A</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.059,276,48.85)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.440,275,45.9)">G</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.498,275,23.9)">C</text> </g> </svg> </TD><TD>1e-5</TD><TD>-1.200e+01</TD><TD>53.33%</TD><TD>2.94%</TD><TD>111.3bp (46.0bp)</TD><TD>Unknown6/Drosophila-Promoters/Homer(0.818)<BR/><A target="_blank" HREF="homerResults/motif1.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif1.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif1.motif">motif file (matrix)</A></TD></TR> <TR><TD>2 <FONT color="red">*</FONT></TD><TD><svg width="205" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,2,49)">A</text> <text fill="#0000EE" x="0" 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fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,75,48.95)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,76,48.9)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.997,75,48.85)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,102,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,100,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,100,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.997,101,48.85)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,127,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,125,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.165,125,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.833,126,40.65)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,152,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,150,48.95)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.073,151,48.9)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.925,150,45.25)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,176,49)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.041,175,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.074,175,46.9)">G</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.884,177,43.2)">A</text> </g> </svg> </TD><TD>1e-4</TD><TD>-1.139e+01</TD><TD>46.67%</TD><TD>1.47%</TD><TD>122.7bp (0.0bp)</TD><TD>NAC078/MA1677.1/Jaspar(0.916)<BR/><A target="_blank" HREF="homerResults/motif2.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif2.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif2.motif">motif file (matrix)</A></TD></TR> <TR><TD>3 <FONT color="red">*</FONT></TD><TD><svg width="255" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,0,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,0,48.95)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.199,1,48.9)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.799,2,38.95)">A</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,25,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.997,26,48.85)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,52,49)">A</text> <text fill="#0000EE" x="0" y="0" 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transform="matrix(0.53,0,0,0.001,202,49)">A</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,201,48.95)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.199,200,48.9)">G</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.799,200,38.95)">C</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,225,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,225,48.95)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,226,48.9)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.997,227,48.85)">A</text> </g> </svg> </TD><TD>1e-3</TD><TD>-9.177e+00</TD><TD>33.33%</TD><TD>0.00%</TD><TD>121.8bp (0.0bp)</TD><TD>PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer(0.746)<BR/><A target="_blank" HREF="homerResults/motif3.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif3.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif3.motif">motif file (matrix)</A></TD></TR> <TR><TD>4 <FONT color="red">*</FONT></TD><TD><svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,2,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,0,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.014,0,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.984,1,48.2)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,48.95)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.132,25,48.9)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.866,26,42.3)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,50,49)">G</text> 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target="_blank" HREF="homerResults/motif9.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif9.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif9.motif">motif file (matrix)</A></TD></TR> <TR><TD>10 <FONT color="red">*</FONT></TD><TD><svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,0,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,0,48.95)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,1,48.9)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.997,2,48.85)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,25,48.95)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,26,48.9)">T</text> <text fill="#00BB00" 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target="_blank" HREF="homerResults/motif11.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif11.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif11.motif">motif file (matrix)</A></TD></TR> </TABLE> <P></P> </BODY></HTML>