meme-output-example.html

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<!---#### $Id: meme-output-example.html 1339 2006-09-21 19:46:28Z tbailey $#### $Log$## Revision 1.5  2006/01/03 01:56:14  tbailey## Fix documentation of PSSM and PSPM in meme-explanation.html and## meme-output-example.html.#### Revision 1.4  2005/08/24 05:31:24  nadya## update references to other thml files. use local urls.#### Revision 1.3  2005/08/24 05:28:16  nadya## update links#### Revision 1.2  2005/08/10 21:02:05  nadya## update path#### Revision 1.1.1.1  2005/07/31 20:18:20  nadya## Importing from meme-3.0.14, and adding configure/make####---><HTML><HEAD><TITLE>MEME</TITLE></HEAD><BODY BGCOLOR=#D5F0FF><A NAME=top_buttons><TABLE ALIGN=LEFT CELLSPACING=0><TR>  <TD BGCOLOR=#DDDDFF><A HREF=#command><B>Command line</B></A>  <TD BGCOLOR=#00FFFF><A HREF=#sequences><B>Training Set</B></A>  <TD BGCOLOR=#DDFFDD><A HREF=#summary1><B>First Motif</B></A>  <TD BGCOLOR=#FFDDFF><A HREF=#motif-summary><B>Summary of Motifs</B></A>  <TD BGCOLOR=#00FF00><A HREF=#stopped><B>Termination</B></A>  <TD BGCOLOR=#FFFF00><A HREF=#explanation><B>Explanation</B></A></TABLE><BR CLEAR=LEFT><FORM ENCTYPE = "application/x-www-form-urlencoded" METHOD = POSTACTION = "cgi-bin/process_request.cgi"><B><BR><INPUT TYPE = SUBMIT NAME = action VALUE = 'MAST'> Search sequence databases with these motifs using <A HREF='mast-intro.html'>MAST.</A><BR><INPUT TYPE = SUBMIT NAME = action VALUE = 'BLOCKS'> Submit these motifs to <A HREF='http://blocks.fhcrc.org/blocks/process_blocks.html'>BLOCKS multiple alignment processor.</A><BR><INPUT TYPE = SUBMIT NAME = action VALUE = 'MetaMEME'> Build and use a motif-based hidden Markov model (HMM) using <A HREF='http://metameme.sdsc.edu'>Meta-MEME.</A> </B><BR CLEAR=LEFT><CENTER><H3><A NAME=version><HR></A><A HREF=#version_doc>MEME - Motif discovery tool</A> <HR></H3></CENTER><P>MEME version 3.0 (Release date: 2001/03/03 13:05:22)<P>For further information on how to interpret these results or to geta copy of the MEME software please access <A HREF=http://meme.nbcr.net>http://meme.nbcr.net</A>.<P>This file may be used as input to the MAST algorithm for searchingsequence databases for matches to groups of motifs.  MAST is availablefor interactive use and downloading at <A HREF=http://meme.nbcr.net>http://meme.nbcr.net</A>.<CENTER><H3><A NAME=reference><HR></A><A HREF=#reference_doc>REFERENCE</A> <HR></H3></CENTER><P>If you use this program in your research, please cite:<P>Timothy L. Bailey and Charles Elkan,"Fitting a mixture model by expectation maximization to discovermotifs in biopolymers", Proceedings of the Second InternationalConference on Intelligent Systems for Molecular Biology, pp. 28-36,AAAI Press, Menlo Park, California, 1994.<CENTER><H3><A NAME=sequences><HR></A><A HREF=#sequences_doc>TRAINING SET</A> <HR></H3></CENTER><PRE>DATAFILE= D:\seqsALPHABET= ACDEFGHIKLMNPQRSTVWYSequence name           Weight Length  Sequence name           Weight Length  -------------           ------ ------  -------------           ------ ------  ICYA_MANSE              1.0000    189  LACB_BOVIN              1.0000    178  BBP_PIEBR               1.0000    173  RETB_BOVIN              1.0000    183  MUP2_MOUSE              1.0000    180  </PRE><INPUT TYPE = HIDDEN NAME = name VALUE = "D:\seqs" ><INPUT TYPE = HIDDEN NAME = alphabet VALUE = "ACDEFGHIKLMNPQRSTVWY" ><INPUT TYPE = HIDDEN NAME = url VALUE = "http://meme.nbcr.net/meme" ><CENTER><H3><A NAME=command><HR></A><A HREF=#command_doc>COMMAND LINE SUMMARY</A> <HR></H3></CENTER><PRE>This information can also be useful in the event you wish to report aproblem with the MEME software.command: meme meme.6266.data -protein -mod zoops -nmotifs 3 -minw 6 -maxw 50 -evt 10000 -time 7200 -nostatus -maxiter 20 model:  mod=         zoops    nmotifs=         3    evt=         10000object function=  E-value of product of p-valueswidth:  minw=            6    maxw=           50    minic=        0.00width:  wg=             11    ws=              1    endgaps=       yesnsites: minsites=        2    maxsites=        5    wnsites=       0.8theta:  prob=            1    spmap=         pam    spfuzz=        120em:     prior=       megap    b=            4515    maxiter=        20        distance=    1e-05data:   n=             903    N=               5sample: seed=            0    seqfrac=         1Dirichlet mixture priors file: prior30.plibLetter frequencies in dataset:A 0.072 C 0.029 D 0.069 E 0.078 F 0.043 G 0.058 H 0.025 I 0.048 K 0.086 L 0.087 M 0.018 N 0.053 P 0.032 Q 0.029 R 0.031 S 0.059 T 0.048 V 0.070 W 0.017 Y 0.050 Background letter frequencies (from dataset with add-one prior applied):A 0.072 C 0.029 D 0.068 E 0.077 F 0.043 G 0.057 H 0.026 I 0.048 K 0.086 L 0.087 M 0.018 N 0.053 P 0.033 Q 0.029 R 0.031 S 0.059 T 0.048 V 0.069 W 0.017 Y 0.050 </PRE><CENTER><H3><A NAME=summary1><HR></A><A HREF=#summary_doc><TABLE ALIGN=LEFT CELLSPACING=0><TR>  <TD BGCOLOR=#OOFFFF><A HREF=#motif-summary><B>P</B></A>  <TD BGCOLOR=#FFFFOO><A HREF=#summary2><B>N</B></A></TABLE>MOTIF  1</A>  &nbsp&nbsp&nbsp width = 26     &nbsp&nbsp&nbsp sites =   5    &nbsp&nbsp&nbsp llr = 244    &nbsp&nbsp&nbsp E-value = 5.0e-006<BR CLEAR=LEFT><HR></H3></CENTER><TABLE CELLPADDING=0 CELLSPACING=1><TR><TD COLSPAN=8><TH><A NAME=simplified1 HREF=#simplified_doc>Simplified</A><TH ALIGN=RIGHT>A<TH><TD  >:<TD>6<TD>:<TD>:<TD>2<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>2<TD>2<TD>:<TD>6<TD  >:<TD>2<TD>:<TD>:<TD>2<TD>:<TD  >8<TD>:</TR><TR><TD COLSPAN=8><TH><A HREF=#simplified_doc>pos.-specific</A><TH ALIGN=RIGHT>C<TH><TD  >2<TD>:<TD>4<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:</TR><TR><TD COLSPAN=8><TH><A HREF=#simplified_doc>probability</A><TH ALIGN=RIGHT>D<TH><TD  >:<TD>:<TD>:<TD>:<TD>2<TD>:<TD  >:<TD>:<TD>:<TD>2<TD>2<TD>:<TD  >8<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:</TR><TR><TD COLSPAN=8><TH><A HREF=#simplified_doc>matrix</A><TH ALIGN=RIGHT>E<TH><TD  >:<TD>:<TD>2<TD>2<TD>2<TD>:<TD  >:<TD>:<TD>:<TD>2<TD>:<TD>:<TD  >:<TD>:<TD>2<TD>:<TD>:<TD>:<TD  >:<TD>2<TD>:<TD>:<TD>4<TD>:<TD  >:<TD>:</TR><TR><TD COLSPAN=8><TH><TH ALIGN=RIGHT>F<TH><TD  >:<TD>:<TD>:<TD>:<TD>:<TD>2<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>8<TD  >:<TD>:<TD>:<TD>:<TD>4<TD>:<TD  >:<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:</TR><TR><TD COLSPAN=8><TH><TH ALIGN=RIGHT>G<TH><TD  >4<TD>:<TD>:<TD>:<TD>:<TD>:<TD  >:<TD>:<TD>2<TD>:<TD>2<TD>:<TD  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