Author: plessy Date: 2011-11-30 04:19:23 +0000 (Wed, 30 Nov 2011) New Revision: 8711
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1 trunk/packages/primer3/trunk/debian/ntdpal.1.xml trunk/packages/primer3/trunk/debian/oligotm.1 trunk/packages/primer3/trunk/debian/oligotm.1.xml Log: Refreshed nroff manpages after minor corrections. Modified: trunk/packages/primer3/trunk/debian/ntdpal.1 =================================================================== --- trunk/packages/primer3/trunk/debian/ntdpal.1 2011-11-30 03:57:25 UTC (rev 8710) +++ trunk/packages/primer3/trunk/debian/ntdpal.1 2011-11-30 04:19:23 UTC (rev 8711) @@ -1,35 +1,52 @@ +'\" t .\" Title: NTDPAL -.\" Author: -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 05/09/2008 +.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author] +.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/> +.\" Date: 11/30/2011 .\" Manual: Primer3 User Manuals .\" Source: ntdpal 1.1.4 +.\" Language: English .\" -.TH "NTDPAL" "1" "05/09/2008" "ntdpal 1.1.4" "Primer3 User Manuals" +.TH "NTDPAL" "1" "11/30/2011" "ntdpal 1.1.4" "Primer3 User Manuals" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- .SH "NAME" -ntdpal \- Provides Primer3's alignment functionality +ntdpal \- Provides Primer3\*(Aqs alignment functionality .SH "SYNOPSIS" -.HP 7 +.HP \w'\fBntdpal\fR\ 'u \fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR} .SH "DESCRIPTION" .PP -Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\'s alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&. +Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\*(Aqs alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&. .SH "OPTIONS" .PP \fB\-g\fR \fIgval\fR .RS 4 \fIgval\fR -is a (positive) float (\&.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score) +is a (positive) float (\&.01 precision) specifying penalty for creating a gap respectively (the penalties are subtracted from the output score) .RE .PP \fB\-l\fR \fIval\fR .RS 4 \fIlval\fR -is a (positive) float (\&.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score) +is a (positive) float (\&.01 precision) specifying penalty for lengthening a gap respectively (the penalties are subtracted from the output score) .RE .PP \fB\-a\fR @@ -39,7 +56,7 @@ .PP \fB\-e\fR .RS 4 -Causes the end postion of the alignment in both sequences to be printed\&. Do not confuse with the \'e\' +Causes the end position of the alignment in both sequences to be printed\&. Do not confuse with the \*(Aqe\*(Aq \fImode\fR\&. .RE .PP @@ -82,7 +99,7 @@ \fIG\fR, \fIl\fR, or \fIL\fR -specifying a global, global end\-anchored, local, or local end\-achored alignment respectively\&. For backward compatibility +specifying a global, global end\-anchored, local, or local end\-anchored alignment respectively\&. For backward compatibility \fIe\fR is equivalent to \fIG\fR\&. @@ -96,16 +113,15 @@ \fBprimer3_core\fR(1) \fBoligotm\fR(1) .SH "COPYRIGHT" +.br Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky .br .PP All rights reserved\&. On Debian\-based systems, please consult -\fI/usr/share/doc/primer3/copyright\fR +/usr/share/doc/primer3/copyright to read the licence of ntdpal\&. .PP -This manual page was written by Charles Plessy -<plessy@debian\&.org> -for the +This manual page was written by Charles Plessy <plessy@debian\&.org> for the Debian(TM) system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&. Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml =================================================================== --- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2011-11-30 03:57:25 UTC (rev 8710) +++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2011-11-30 04:19:23 UTC (rev 8711) @@ -41,7 +41,7 @@ </legalnotice> <legalnotice> - <para>This manual page was written by &dhusername; &dhemail; for + <para>This manual page was written by &dhusername; <&dhemail;> for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself.<!-- This also applies to this source document --></para> Modified: trunk/packages/primer3/trunk/debian/oligotm.1 =================================================================== --- trunk/packages/primer3/trunk/debian/oligotm.1 2011-11-30 03:57:25 UTC (rev 8710) +++ trunk/packages/primer3/trunk/debian/oligotm.1 2011-11-30 04:19:23 UTC (rev 8711) @@ -1,19 +1,36 @@ +'\" t .\" Title: OLIGOTM -.\" Author: -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 05/09/2008 +.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author] +.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/> +.\" Date: 11/30/2011 .\" Manual: Primer3 User Manuals .\" Source: oligotm 1.1.4 +.\" Language: English .\" -.TH "OLIGOTM" "1" "05/09/2008" "oligotm 1.1.4" "Primer3 User Manuals" +.TH "OLIGOTM" "1" "11/30/2011" "oligotm 1.1.4" "Primer3 User Manuals" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- .SH "NAME" -oligotm \- Prints oligo's melting temperature on stdout +oligotm \- Prints oligo\*(Aqs melting temperature on stdout .SH "SYNOPSIS" -.HP 8 +.HP \w'\fBoligotm\fR\ 'u \fBoligotm\fR [OPTIONS] {oligo} .PP where oligo is a DNA sequence of between 2 and 36 bases @@ -21,7 +38,7 @@ .PP \fBoligotm\fR -prints the melting temperature of a given desoxyribooligonucleotide on the standard output\&. It is part of the oligotm library\&. +prints the melting temperature of a given deoxyribonucleotide on the standard output\&. It is part of the oligotm library\&. .SH "OPTIONS" .PP \fB\-mv\fR \fImonovalent_conc\fR @@ -36,7 +53,7 @@ .PP \fB\-n\fR \fIdNTP_conc\fR .RS 4 -Concentration of deoxynycleotide triphosphate in mM, by default 0\ \&mM\&. +Concentration of deoxynucleotide triphosphate in mM, by default 0\ \&mM\&. .RE .PP \fB\-d\fR \fIdna_conc\fR @@ -49,14 +66,28 @@ Specifies the table of thermodynamic parameters and the method of melting temperature calculation: .sp .RS 4 -\h'-04'\(bu\h'+03'\fI0\fR +.ie n \{\ +\h'-04'\(bu\h'+03'\c +.\} +.el \{\ +.sp -1 +.IP \(bu 2.3 +.\} +\fI0\fR Breslauer et al\&., 1986 and Rychlik et al\&., 1990 (used by primer3 up to and including release 1\&.1\&.0)\&. This is the default, but \fInot\fR the recommended value\&. .RE .sp .RS 4 -\h'-04'\(bu\h'+03'\fI1\fR +.ie n \{\ +\h'-04'\(bu\h'+03'\c +.\} +.el \{\ +.sp -1 +.IP \(bu 2.3 +.\} +\fI1\fR Use nearest neighbor parameter from SantaLucia 1998\&. \fIThis is the recommended value\fR\&. .RE @@ -67,20 +98,41 @@ Specifies salt correction formula for the melting temperature calculation: .sp .RS 4 -\h'-04'\(bu\h'+03'\fI0\fR +.ie n \{\ +\h'-04'\(bu\h'+03'\c +.\} +.el \{\ +.sp -1 +.IP \(bu 2.3 +.\} +\fI0\fR Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but \fInot\fR the recommended value\&. .RE .sp .RS 4 -\h'-04'\(bu\h'+03'\fI1\fR +.ie n \{\ +\h'-04'\(bu\h'+03'\c +.\} +.el \{\ +.sp -1 +.IP \(bu 2.3 +.\} +\fI1\fR SantaLucia 1998\&. \fIThis is the recommended value\fR\&. .RE .sp .RS 4 -\h'-04'\(bu\h'+03'\fI1\fR +.ie n \{\ +\h'-04'\(bu\h'+03'\c +.\} +.el \{\ +.sp -1 +.IP \(bu 2.3 +.\} +\fI2\fR Owczarzy et al\&., 2004\&. .RE .RE @@ -98,16 +150,15 @@ \fBprimer3_core\fR(1) \fBntdpal\fR(1) .SH "COPYRIGHT" +.br Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky .br .PP All rights reserved\&. On Debian\-based systems, please consult -\fI/usr/share/doc/primer3/copyright\fR +/usr/share/doc/primer3/copyright to read the licence of oligotm\&. .PP -This manual page was written by Charles Plessy -<plessy@debian\&.org> -for the +This manual page was written by Charles Plessy <plessy@debian\&.org> for the Debian(TM) system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&. Modified: trunk/packages/primer3/trunk/debian/oligotm.1.xml =================================================================== --- trunk/packages/primer3/trunk/debian/oligotm.1.xml 2011-11-30 03:57:25 UTC (rev 8710) +++ trunk/packages/primer3/trunk/debian/oligotm.1.xml 2011-11-30 04:19:23 UTC (rev 8711) @@ -41,7 +41,7 @@ </legalnotice> <legalnotice> - <para>This manual page was written by &dhusername; &dhemail; for + <para>This manual page was written by &dhusername; <&dhemail;> for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself.<!-- This also applies to this source document --></para> @@ -145,7 +145,7 @@ <para><parameter>1</parameter> SantaLucia 1998. <emphasis>This is the recommended value</emphasis>.</para> </listitem> <listitem> - <para><parameter>1</parameter> Owczarzy et al., 2004.</para> + <para><parameter>2</parameter> Owczarzy et al., 2004.</para> </listitem> </itemizedlist> </listitem> _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
