motif-format.html
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<!---#### $Id: motif-format.html 1339 2006-09-21 19:46:28Z tbailey $#### $Log$## Revision 1.2 2006/03/07 23:30:20 nadya## merge branches v3_5_1 and v3_5_2 back to the trunk#### Revision 1.1.1.1.6.1 2006/02/22 20:49:02 nadya## enabling styling with js and css#### Revision 1.1.1.1 2005/07/31 20:18:42 nadya## Importing from meme-3.0.14, and adding configure/make####---><HTML><HEAD><TITLE>MAST - Motif Format</TITLE><script src="template-css.js" type="text/javascript"></script></HEAD><body class="body"> <script src="template-header.js" type="text/javascript"></script> <H1>MAST -- Motif Alignment and Search Tool</H1> <H2><I>Motif search tool</I></H2> <HR> <H2> MOTIF FORMAT </H2> <B>MAST can search using (multiple) motifs contained in <UL> <LI> a MEME output file, <LI> a GCG profile file, <LI> two or more GCG profile files concatenated together, or <LI> a file with the following format.</B> </UL> <P> <CENTER> <TABLE BORDER> <CAPTION> <B>Motif file format</B> </CAPTION> <TR> <TD><PRE> ALPHABET= <I>alphabet</I> log-odds matrix: alength= <I>alength</I> w= <I>w</I> <I>row_1 row_2 ... row_w </I> </PRE> </TABLE> <P> </CENTER> <UL> <LI>A motif is represented by a position-dependent scoring matrix. <LI>A scoring matrix is preceded by a line starting with the words <NOBR><TT>log-odds matrix: </TT></NOBR> and specifying <TT><I>alength</I></TT>, the length of the alphabet (number of columns in the scoring matrix), and the <TT><I>w</I></TT>, the width of the motif (number of rows in the scoring matrix). <LI>The following <TT><I>w</I></TT> lines (no blank lines allowed) contain the rows of the scoring matrix. Row <I>i</I>, column <I>j</I> of the matrix gives the score for the <I>j-th</I> letter in <TT><I>alphabet</I></TT> appearing at position <I>i</I> in an occurrence of the motif. <LI>The spaces after the equals signs and the colon are required. <LI>The number of letters in <TT><I>alphabet</I></TT> must equal <TT><I>alength</I></TT>. <LI>Any number of additional motifs may follow the first one. <LI>The motif file must contain a line starting with <PRE> ALPHABET= </PRE> followed by <I>alphabet</I>, a list containing the letters used in the motifs. The order of the letters in <I>alphabet</I> must be the same as the order of the columns of scores in the motifs. The order need not be alphabetical and case does not matter, but there should be no spaces in <I>alphabet</I>. The letters in <I>alphabet</I> must be a subset of either the IUB/IUPAC DNA (<B>ABCDGHKMNRSTUVWY*-</B>) or protein (<B>ABCDEFGHIKLMNPQRSTUVWXYZ*-</B>) alphabets. DNA alphabets must contain at least the letters <B>ACGT</B>. Protein alphabets must contain at least the letters <B>ACDEFGHIKLMNPQRSTVWY</B>. All other letters in the alphabets are optional. If any of the optional letters are missing from <I>alphabet</I>, MAST automatically generates scores for them by taking the weighted average of the scores for the letters which the missing letter could match. (The weights are the frequencies of the replaced letters in the appropriate non-redundant database.) Replacements for the optional letters are given in the following table. <P> <CENTER> <TABLE BORDER> <CAPTION> <B>Letters matched by optional letters</B> </CAPTION> <TR> <TH ROWSPAN=2>optional <BR> letter <TH COLSPAN=2> matches <TR> <TH>DNA <TH>protein <TR> <TD ALIGN=CENTER> B <TD>CGT <TD>DN <TR> <TD ALIGN=CENTER> D <TD>AGT <TD> <TR> <TD ALIGN=CENTER> H <TD>ACT <TD> <TR> <TD ALIGN=CENTER> K <TD>GT <TD> <TR> <TD ALIGN=CENTER> M <TD>AC <TD> <TR> <TD ALIGN=CENTER> N <TD>ACGT <TD> <TR> <TD ALIGN=CENTER> R <TD>AG <TD> <TR> <TD ALIGN=CENTER> S <TD>CG <TD> <TR> <TD ALIGN=CENTER> U <TD>T <TD>ACDEFGHIKLMNPQRSTVWY <TR> <TD ALIGN=CENTER> V <TD>CAG <TD> <TR> <TD ALIGN=CENTER> W <TD>AT <TD> <TR> <TD ALIGN=CENTER> X <TD> <TD>ACDEFGHIKLMNPQRSTVWY <TR> <TD ALIGN=CENTER> Y <TD>CT <TD> <TR> <TD ALIGN=CENTER> Z <TD> <TD>EQ <TR> <TD ALIGN=CENTER><FONT SIZE=+1>*</FONT> <TD>ACGT <TD>ACDEFGHIKLMNPQRSTVWY <TR> <TD ALIGN=CENTER><FONT SIZE=+1>-</FONT> <TD>ACGT <TD>ACDEFGHIKLMNPQRSTVWY </TABLE> </CENTER> </UL> <P> <H2> EXAMPLE </H2> <font><B>Here is an example of a DNA motif file that contains two motifs.</B></font> <P> <center> <h3>Sample motif file</h3> <TABLE BORDER> <TR> <TD><PRE> ALPHABET= ACGT log-odds matrix: alength= 4 w= 9 -4.275 -0.182 -4.195 1.408 -4.296 -1.487 1.880 -0.816 -2.160 -1.492 -4.171 1.474 -0.810 -4.076 1.872 -2.164 1.537 -1.487 -4.195 -4.205 0.113 0.340 -0.237 -0.209 -0.454 0.923 0.390 -0.834 -1.336 -0.082 0.905 0.100 0.674 -4.183 0.130 -0.201 log-odds matrix: alength= 4 w= 6 -2.032 0.324 1.371 -0.781 -0.409 0.560 -0.250 0.119 -4.274 -0.519 -0.260 1.167 -2.188 2.300 -4.191 -2.465 1.265 -4.111 -0.267 -2.180 -1.977 2.158 -1.661 -2.071 </PRE> </TABLE> </center> <P> </CENTER> In the example above, because the order of the letters in <TT><I>alphabet</I></TT> is <I>ACGT</I>, the first column of each motif gives the scores for the letter <I>A</I> at each position in the motif, the second column gives the scores for <I>C</I> and so forth. <HR> <P> <A href="mast-input.html"><B>MAST input</B></A> <P> <A href="mast-intro.html"><B>MAST introduction</B></A> <HR><script src="template-footer.js" type="text/javascript"></script></BODY></HTML>⌨️ 快捷键说明
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