[med-svn] r8711 - trunk/packages/primer3/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Wed Nov 30 04:19:23 UTC 2011
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 at debian\&.org>
-for the
+This manual page was written by Charles Plessy <plessy at 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 at debian\&.org>
-for the
+This manual page was written by Charles Plessy <plessy at 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>
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