[Pkg-emboss-commits] r121 - / embassy-meme embassy-meme/trunk embassy-meme/trunk/debian embassy-meme/trunk/debian/manpages
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Nov 3 07:38:02 UTC 2007
Author: charles-guest
Date: 2007-11-03 07:38:02 +0000 (Sat, 03 Nov 2007)
New Revision: 121
Added:
embassy-meme/
embassy-meme/trunk/
embassy-meme/trunk/debian/
embassy-meme/trunk/debian/changelog
embassy-meme/trunk/debian/control
embassy-meme/trunk/debian/embassy-meme.manpages
embassy-meme/trunk/debian/manpages/
embassy-meme/trunk/debian/manpages/emast.1e
embassy-meme/trunk/debian/manpages/ememe.1e
embassy-meme/trunk/debian/rules
embassy-meme/trunk/debian/watch
Log:
Work in progress, untested and not yet built.
Added: embassy-meme/trunk/debian/changelog
===================================================================
--- embassy-meme/trunk/debian/changelog (rev 0)
+++ embassy-meme/trunk/debian/changelog 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,5 @@
+embassy-meme (0.1.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 03 Nov 2007 15:51:58 +0900
Added: embassy-meme/trunk/debian/control
===================================================================
--- embassy-meme/trunk/debian/control (rev 0)
+++ embassy-meme/trunk/debian/control 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,18 @@
+Source: embassy-meme
+Section: science
+Priority: optional
+Build-depends: cdbs, debhelper (>= 5), libajax5-dev, libnucleus5-dev, emboss-lib
+Maintainer: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+XS-Vcs-Browser: http://svn.debian.org/wsvn/pkg-emboss/embassy-domalign/trunk/debian
+XS-Vcs-Svn: svn://svn.debian.org/svn/pkg-emboss/embassy-domalign
+Standards-Version: 3.7.2
+Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#MEME
+
+Package: embassy-meme
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: emboss
+Suggests: embassy
+Description: EMBOSS wrapper for MEME
+ (to be completed)
Added: embassy-meme/trunk/debian/embassy-meme.manpages
===================================================================
--- embassy-meme/trunk/debian/embassy-meme.manpages (rev 0)
+++ embassy-meme/trunk/debian/embassy-meme.manpages 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,2 @@
+debian/manpages/emast.1e
+debian/manpages/ememe.1e
Added: embassy-meme/trunk/debian/manpages/emast.1e
===================================================================
--- embassy-meme/trunk/debian/manpages/emast.1e (rev 0)
+++ embassy-meme/trunk/debian/manpages/emast.1e 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,196 @@
+.\" Title: EMAST
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 11/03/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "EMAST" "1e" "11/03/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+emast \- Motif detection
+.SH "SYNOPSIS"
+.HP 6
+\fBemast\fR \fB\-mfile\ \fR\fB\fIinfile\fR\fR [\fB\-d\ \fR\fB\fIinfile\fR\fR] [\fB\-a\ \fR\fB\fIinfile\fR\fR] [\fB\-bfile\ \fR\fB\fIinfile\fR\fR] \fB\-ev\ \fR\fB\fIfloat\fR\fR \fB\-mt\ \fR\fB\fIfloat\fR\fR [\fB\-smax\ \fR\fB\fIinteger\fR\fR] [\fB\-stdin\ \fR\fB\fIboolean\fR\fR] [\fB\-text\ \fR\fB\fIboolean\fR\fR] [\fB\-dna\ \fR\fB\fIboolean\fR\fR] [\fB\-comp\ \fR\fB\fIboolean\fR\fR] [\fB\-rank\ \fR\fB\fIinteger\fR\fR] [\fB\-best\ \fR\fB\fIboolean\fR\fR] [\fB\-remcorr\ \fR\fB\fIboolean\fR\fR] [\fB\-brief\ \fR\fB\fIboolean\fR\fR] [\fB\-b\ \fR\fB\fIboolean\fR\fR] [\fB\-nostatus\ \fR\fB\fIboolean\fR\fR] [\fB\-hitlist\ \fR\fB\fIboolean\fR\fR] \fB\-c\ \fR\fB\fIinteger\fR\fR \fB\-sep\ \fR\fB\fIboolean\fR\fR \fB\-norc\ \fR\fB\fIboolean\fR\fR \fB\-w\ \fR\fB\fIboolean\fR\fR \fB\-seqp\ \fR\fB\fIboolean\fR\fR \fB\-mf\ \fR\fB\fIstring\fR\fR \fB\-df\ \fR\fB\fIstring\fR\fR \fB\-minseqs\ \fR\fB\fIinteger\fR\fR \fB\-mev\ \fR\fB\fIfloat\fR\fR \fB\-m\ \fR\fB\fIinteger\fR\fR \fB\-diag\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 6
+\fBemast\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBemast\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq). It is part of the "Protein:Motifs" command group(s).
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-mfile\fR \fIinfile\fR
+.RS 4
+If \-d <database> is not given, MAST looks for database specified inside of <mfile>.
+.RE
+.PP
+\fB\-d\fR \fIinfile\fR
+.RS 4
+If \-d <database> is not given, MAST looks for database specified inside of <mfile>.
+.RE
+.PP
+\fB\-a\fR \fIinfile\fR
+.RS 4
+Input file <mfile> is assumed to contain motifs in the format output by bin/make_logodds and <a> is their alphabet; \-d <database> or \-stdin must be specified when this option is used.
+.RE
+.PP
+\fB\-bfile\fR \fIinfile\fR
+.RS 4
+The random model uses the letter frequencies given in <bfile> instead of the non\-redundant database frequencies. The format of <bfile> is the same as that for the MEME \-bfile opton; see the MEME documentation for details. Sample files are given in directory tests: tests/nt.freq and tests/na.freq in the MEME distribution.)
+.RE
+.SS "Required section"
+.PP
+\fB\-ev\fR \fIfloat\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-mt\fR \fIfloat\fR
+.RS 4
+Default value: 0.0001
+.RE
+.SS "Additional section"
+.PP
+\fB\-smax\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-stdin\fR \fIboolean\fR
+.RS 4
+The default is to read the database specified inside <mfile>. Default value: N
+.RE
+.PP
+\fB\-text\fR \fIboolean\fR
+.RS 4
+Default is hypertext (HTML) format Default value: N
+.RE
+.PP
+\fB\-dna\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-comp\fR \fIboolean\fR
+.RS 4
+The random model uses the letter frequencies in the current target sequence instead of the non\-redundant database frequencies. This causes p\-values and E\-values to be compensated individually for the actual composition of each sequence in the database. This option can increase search time substantially due to the need to compute a different score distribution for each high\-scoring sequence. Default value: N
+.RE
+.PP
+\fB\-rank\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-best\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-remcorr\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-brief\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-b\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-nostatus\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-hitlist\fR \fIboolean\fR
+.RS 4
+If you specify the \-hitlist switch to MAST, the motif 'diagram' takes the form of a comma separated list of motif occurrences ('hits'). Each 'hit' has the format: <strand><motif> <start> <end> <p\-value> where <strand> is the strand (+ or \- for DNA, blank for protein), <motif> is the motif number, <start> is the starting position of the hit, <end> is the ending position of the hit, and <p\-value> is the position p\-value of the hit. Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-c\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-sep\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-norc\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-w\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-seqp\fR \fIboolean\fR
+.RS 4
+The default is to use POSITION p\-values. Default value: N
+.RE
+.PP
+\fB\-mf\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-df\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-minseqs\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-mev\fR \fIfloat\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-m\fR \fIinteger\fR
+.RS 4
+Overrides value set by using \-mev. Default value: \-1
+.RE
+.PP
+\fB\-diag\fR \fIstring\fR
+.RS 4
+See on\-line documentation for a valid example.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).
+.SH "SEE ALSO"
+.PP
+emast is fully documented via the
+\fBtfm\fR(1)
+system.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists.alioth.debian.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
+.br
Added: embassy-meme/trunk/debian/manpages/ememe.1e
===================================================================
--- embassy-meme/trunk/debian/manpages/ememe.1e (rev 0)
+++ embassy-meme/trunk/debian/manpages/ememe.1e 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,212 @@
+.\" Title: EMEME
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 11/03/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "EMEME" "1e" "11/03/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+ememe \- Motif detection
+.SH "SYNOPSIS"
+.HP 6
+\fBememe\fR \fB\-dataset\ \fR\fB\fIseqset\fR\fR [\fB\-bfile\ \fR\fB\fIinfile\fR\fR] [\fB\-plib\ \fR\fB\fIinfile\fR\fR] [\fB\-mod\ \fR\fB\fIselection\fR\fR] [\fB\-nmotifs\ \fR\fB\fIinteger\fR\fR] [\fB\-text\ \fR\fB\fIboolean\fR\fR] [\fB\-prior\ \fR\fB\fIselection\fR\fR] [\fB\-evt\ \fR\fB\fIfloat\fR\fR] [\fB\-nsites\ \fR\fB\fIinteger\fR\fR] [\fB\-minsites\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsites\ \fR\fB\fIinteger\fR\fR] [\fB\-wnsites\ \fR\fB\fIfloat\fR\fR] [\fB\-w\ \fR\fB\fIinteger\fR\fR] [\fB\-minw\ \fR\fB\fIinteger\fR\fR] [\fB\-maxw\ \fR\fB\fIinteger\fR\fR] [\fB\-nomatrim\ \fR\fB\fIboolean\fR\fR] [\fB\-wg\ \fR\fB\fIinteger\fR\fR] [\fB\-ws\ \fR\fB\fIinteger\fR\fR] [\fB\-noendgaps\ \fR\fB\fIboolean\fR\fR] [\fB\-revcomp\ \fR\fB\fIboolean\fR\fR] [\fB\-pal\ \fR\fB\fIboolean\fR\fR] [\fB\-nostatus\ \fR\fB\fIboolean\fR\fR] \fB\-maxiter\ \fR\fB\fIinteger\fR\fR \fB\-distance\ \fR\fB\fIfloat\fR\fR \fB\-b\ \fR\fB\fIfloat\fR\fR \fB\-spfuzz\ \fR\fB\fIfloat\fR\fR \fB\-spmap\ \fR\fB\fIselection\fR\fR \fB\-cons\ \fR\fB\fIstring\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-p\ \fR\fB\fIinteger\fR\fR \fB\-time\ \fR\fB\fIinteger\fR\fR \fB\-sf\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 6
+\fBememe\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBememe\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq). It is part of the "Protein:Motifs" command group(s).
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dataset\fR \fIseqset\fR
+.RS 4
+User must provide the full filename of a set of sequences, not an indirect reference, e.g. a USA is NOT acceptable.
+.RE
+.PP
+\fB\-bfile\fR \fIinfile\fR
+.RS 4
+The name of the file containing the background model for sequences. The background model is the model of random sequences used by MEME. The background model is used by MEME 1) during EM as the 'null model', 2) for calculating the log likelihood ratio of a motif, 3) for calculating the significance (E\-value) of a motif, and, 4) for creating the position\-specific scoring matrix (log\-odds matrix). See application documentation for more information.
+.RE
+.PP
+\fB\-plib\fR \fIinfile\fR
+.RS 4
+The name of the file containing the Dirichlet prior in the format of file prior30.plib
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-mod\fR \fIselection\fR
+.RS 4
+If you know how occurrences of motifs are distributed in the training set sequences, you can specify it with these options. The default distribution of motif occurrences is assumed to be zero or one occurrence of per sequence. oops : One Occurrence Per Sequence. MEME assumes that each sequence in the dataset contains exactly one occurrence of each motif. This option is the fastest and most sensitive but the motifs returned by MEME may be 'blurry' if any of the sequences is missing them. zoops : Zero or One Occurrence Per Sequence. MEME assumes that each sequence may contain at most one occurrence of each motif. This option is useful when you suspect that some motifs may be missing from some of the sequences. In that case, the motifs found will be more accurate than using the first option. This option takes more computer time than the first option (about twice as much) and is slightly less sensitive to weak motifs present in all of the sequences. anr : Any Number of Repetitions. MEME assumes each sequence may contain any number of non\-overlapping occurrences of each motif. This option is useful when you suspect that motifs repeat multiple times within a single sequence. In that case, the motifs found will be much more accurate than using one of the other options. This option can also be used to discover repeats within a single sequence. This option takes the much more computer time than the first option (about ten times as much) and is somewhat less sensitive to weak motifs which do not repeat within a single sequence than the other two options. Default value: zoops
+.RE
+.PP
+\fB\-nmotifs\fR \fIinteger\fR
+.RS 4
+The number of *different* motifs to search for. MEME will search for and output <n> motifs. Default value: 1
+.RE
+.PP
+\fB\-text\fR \fIboolean\fR
+.RS 4
+Default output is in HTML Default value: N
+.RE
+.PP
+\fB\-prior\fR \fIselection\fR
+.RS 4
+The prior distribution on the model parameters. dirichlet: Simple Dirichlet prior. This is the default for \-dna and \-alph. It is based on the non\-redundant database letter frequencies. dmix: Mixture of Dirichlets prior. This is the default for \-protein. mega: Extremely low variance dmix; variance is scaled inversely with the size of the dataset. megap: Mega for all but last iteration of EM; dmix on last iteration. addone: Add +1 to each observed count. Default value: dirichlet
+.RE
+.PP
+\fB\-evt\fR \fIfloat\fR
+.RS 4
+Quit looking for motifs if E\-value exceeds this value. Has an extremely high default so by default MEME never quits before \-nmotifs <n> have been found. Default value: \-1
+.RE
+.PP
+\fB\-nsites\fR \fIinteger\fR
+.RS 4
+These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for \-nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between \-minsites and \-maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for \-minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of \-minsites is equal to sqrt(number sequences). The hardcoded default value of \-maxsites is equal to the number of sequences (zoops) or MIN(5* num.sequences, 50) (anr). Default value: \-1
+.RE
+.PP
+\fB\-minsites\fR \fIinteger\fR
+.RS 4
+These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for \-nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between \-minsites and \-maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for \-minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of \-minsites is equal to sqrt(number sequences). The hardcoded default value of \-maxsites is equal to the number of sequences (zoops) or MIN(5 * num.sequences, 50) (anr). Default value: \-1
+.RE
+.PP
+\fB\-maxsites\fR \fIinteger\fR
+.RS 4
+These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for \-nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between \-minsites and \-maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for \-minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of \-minsites is equal to sqrt(number sequences). The hardcoded default value of \-maxsites is equal to the number of sequences (zoops) or MIN(5 * num.sequences, 50) (anr). Default value: \-1
+.RE
+.PP
+\fB\-wnsites\fR \fIfloat\fR
+.RS 4
+The weight on the prior on nsites. This controls how strong the bias towards motifs with exactly nsites sites (or between minsites and maxsites sites) is. It is a number in the range [0..1). The larger it is, the stronger the bias towards motifs with exactly nsites occurrences is. Default value: .8
+.RE
+.PP
+\fB\-w\fR \fIinteger\fR
+.RS 4
+The width of the motif(s) to search for. If \-w is given, only that width is tried. Otherwise, widths between \-minw and \-maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value. Default value: \-1
+.RE
+.PP
+\fB\-minw\fR \fIinteger\fR
+.RS 4
+The width of the motif(s) to search for. If \-w is given, only that width is tried. Otherwise, widths between \-minw and \-maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value. Default value: 8
+.RE
+.PP
+\fB\-maxw\fR \fIinteger\fR
+.RS 4
+The width of the motif(s) to search for. If \-w is given, only that width is tried. Otherwise, widths between \-minw and \-maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value. Default value: 50
+.RE
+.PP
+\fB\-nomatrim\fR \fIboolean\fR
+.RS 4
+The \-nomatrim, \-wg, \-ws and \-noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying \-nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches \-wg (gap cost), \-ws (space cost) and \-noendgaps (do not penalize endgaps). See application documentation for further information. Default value: N
+.RE
+.PP
+\fB\-wg\fR \fIinteger\fR
+.RS 4
+The \-nomatrim, \-wg, \-ws and \-noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying \-nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches \-wg (gap cost), \-ws (space cost) and \-noendgaps (do not penalize endgaps). See application documentation for further information. Default value: 11
+.RE
+.PP
+\fB\-ws\fR \fIinteger\fR
+.RS 4
+The \-nomatrim, \-wg, \-ws and \-noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying \-nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches \-wg (gap cost), \-ws (space cost) and \-noendgaps (do not penalize endgaps). See application documentation for further information. Default value: 1
+.RE
+.PP
+\fB\-noendgaps\fR \fIboolean\fR
+.RS 4
+The \-nomatrim, \-wg, \-ws and \-noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying \-nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches \-wg (gap cost), \-ws (space cost) and \-noendgaps (do not penalize endgaps). See application documentation for further information. Default value: N
+.RE
+.PP
+\fB\-revcomp\fR \fIboolean\fR
+.RS 4
+Motifs occurrences may be on the given DNA strand or on its reverse complement. The default is to look for DNA motifs only on the strand given in the training set. Default value: N
+.RE
+.PP
+\fB\-pal\fR \fIboolean\fR
+.RS 4
+Choosing \-pal causes MEME to look for palindromes in DNA datasets. MEME averages the letter frequencies in corresponding columns of the motif (PSPM) together. For instance, if the width of the motif is 10, columns 1 and 10, 2 and 9, 3 and 8, etc., are averaged together. The averaging combines the frequency of A in one column with T in the other, and the frequency of C in one column with G in the other. Default value: N
+.RE
+.PP
+\fB\-nostatus\fR \fIboolean\fR
+.RS 4
+Set this option to print a progress report to the terminal. Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-maxiter\fR \fIinteger\fR
+.RS 4
+The number of iterations of EM to run from any starting point. EM is run for <n> iterations or until convergence (see \-distance, below) from each starting point. Default value: 50
+.RE
+.PP
+\fB\-distance\fR \fIfloat\fR
+.RS 4
+The convergence criterion. MEME stops iterating EM when the change in the motif frequency matrix is less than <a>. (Change is the euclidean distance between two successive frequency matrices.) Default value: 0.001
+.RE
+.PP
+\fB\-b\fR \fIfloat\fR
+.RS 4
+The strength of the prior on model parameters. A value of 0 means use intrinsic strength of prior if prior = dmix. The default values are 0.01 if prior = dirichlet or 0 if prior = dmix. These defaults are hardcoded into MEME (the value of the default in the ACD file is not used). Default value: \-1.0
+.RE
+.PP
+\fB\-spfuzz\fR \fIfloat\fR
+.RS 4
+The fuzziness of the mapping. Possible values are greater than 0. Meaning depends on \-spmap, see below. See the application documentation for more information. Default value: \-1.0
+.RE
+.PP
+\fB\-spmap\fR \fIselection\fR
+.RS 4
+The type of mapping function to use. uni: Use prior when converting a substring to an estimate of theta. Default \-spfuzz <a>: 0.5. pam: Use columns of PAM <a> matrix when converting a substring to an estimate of theta. Default \-spfuzz <a>: 120 (PAM 120). See the application documentation for more information. Default value: uni
+.RE
+.PP
+\fB\-cons\fR \fIstring\fR
+.RS 4
+Override the sampling of starting points and just use a starting point derived from <string>. This is useful when an actual occurrence of a motif is known and can be used as the starting point for finding the motif. See the application documentation for more information.
+.RE
+.PP
+\fB\-maxsize\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-p\fR \fIinteger\fR
+.RS 4
+Only values of >0 will be applied. The \-p <np> argument causes a version of MEME compiled for a parallel CPU architecture to be run. (By placing <np> in quotes you may pass installation specific switches to the 'mpirun' command. The number of processors to run on must be the first argument following \-p).
+.RE
+.PP
+\fB\-time\fR \fIinteger\fR
+.RS 4
+Only values of more than 0 will be applied.
+.RE
+.PP
+\fB\-sf\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).
+.SH "SEE ALSO"
+.PP
+ememe is fully documented via the
+\fBtfm\fR(1)
+system.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists.alioth.debian.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
+.br
Added: embassy-meme/trunk/debian/rules
===================================================================
--- embassy-meme/trunk/debian/rules (rev 0)
+++ embassy-meme/trunk/debian/rules 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
Property changes on: embassy-meme/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: embassy-meme/trunk/debian/watch
===================================================================
--- embassy-meme/trunk/debian/watch (rev 0)
+++ embassy-meme/trunk/debian/watch 2007-11-03 07:38:02 UTC (rev 121)
@@ -0,0 +1,2 @@
+version=3
+ftp://emboss.open-bio.org/pub/EMBOSS/MEME-(.*)\.tar\.gz
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