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165 lines
4.2 KiB
Groff
165 lines
4.2 KiB
Groff
'\" t
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.\" Title: OLIGOTM
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.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
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.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
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.\" Date: 11/30/2011
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.\" Manual: Primer3 User Manuals
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.\" Source: oligotm 1.1.4
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.\" Language: English
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.\"
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.TH "OLIGOTM" "1" "11/30/2011" "oligotm 1.1.4" "Primer3 User Manuals"
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.\" -----------------------------------------------------------------
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.\" * Define some portability stuff
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.\" -----------------------------------------------------------------
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.\" http://bugs.debian.org/507673
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.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.ie \n(.g .ds Aq \(aq
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.el .ds Aq '
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.\" -----------------------------------------------------------------
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.\" * set default formatting
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.\" -----------------------------------------------------------------
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.\" disable hyphenation
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.nh
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.\" disable justification (adjust text to left margin only)
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.ad l
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.\" -----------------------------------------------------------------
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.\" * MAIN CONTENT STARTS HERE *
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.\" -----------------------------------------------------------------
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.SH "NAME"
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oligotm \- Prints oligo\*(Aqs melting temperature on stdout
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.SH "SYNOPSIS"
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.HP \w'\fBoligotm\fR\ 'u
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\fBoligotm\fR [OPTIONS] {oligo}
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.PP
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where oligo is a DNA sequence of between 2 and 36 bases
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.SH "DESCRIPTION"
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.PP
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\fBoligotm\fR
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prints the melting temperature of a given deoxyribonucleotide on the standard output\&. It is part of the oligotm library\&.
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.SH "OPTIONS"
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.PP
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\fB\-mv\fR \fImonovalent_conc\fR
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.RS 4
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Concentration of monovalent cations in mM, by default 50\ \&mM\&.
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.RE
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.PP
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\fB\-dv\fR \fIdivalent_conc\fR
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.RS 4
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Concentration of divalent cations in mM, by default 0\ \&mM\&.
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.RE
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.PP
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\fB\-n\fR \fIdNTP_conc\fR
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.RS 4
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Concentration of deoxynucleotide triphosphate in mM, by default 0\ \&mM\&.
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.RE
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.PP
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\fB\-d\fR \fIdna_conc\fR
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.RS 4
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Concentration of DNA strands in nM, by default 50\ \&nM\&.
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.RE
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.PP
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\fB\-tp\fR \fI[0|1]\fR
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.RS 4
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Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
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.sp
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.RS 4
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.ie n \{\
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\h'-04'\(bu\h'+03'\c
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.\}
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.el \{\
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.sp -1
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.IP \(bu 2.3
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.\}
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\fI0\fR
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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
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\fInot\fR
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the recommended value\&.
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.RE
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.sp
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.RS 4
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.ie n \{\
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\h'-04'\(bu\h'+03'\c
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.\}
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.el \{\
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.sp -1
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.IP \(bu 2.3
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.\}
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\fI1\fR
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Use nearest neighbor parameter from SantaLucia 1998\&.
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\fIThis is the recommended value\fR\&.
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.RE
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.RE
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.PP
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\fB\-sc\fR \fI[0\&.\&.2]\fR
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.RS 4
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Specifies salt correction formula for the melting temperature calculation:
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.sp
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.RS 4
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.ie n \{\
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\h'-04'\(bu\h'+03'\c
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.\}
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.el \{\
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.sp -1
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.IP \(bu 2.3
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.\}
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\fI0\fR
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Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
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\fInot\fR
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the recommended value\&.
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.RE
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.sp
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.RS 4
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.ie n \{\
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\h'-04'\(bu\h'+03'\c
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.\}
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.el \{\
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.sp -1
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.IP \(bu 2.3
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.\}
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\fI1\fR
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SantaLucia 1998\&.
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\fIThis is the recommended value\fR\&.
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.RE
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.sp
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.RS 4
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.ie n \{\
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\h'-04'\(bu\h'+03'\c
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.\}
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.el \{\
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.sp -1
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.IP \(bu 2.3
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.\}
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\fI2\fR
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Owczarzy et al\&., 2004\&.
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.RE
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.RE
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.PP
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\fB\-i\fR
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.RS 4
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prints references to publications which were used for thermodynamic calculations\&.
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.RE
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.SH "REFERENCE"
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.PP
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Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
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.SH "SEE ALSO"
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.PP
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\fBprimer3_core\fR(1)
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\fBntdpal\fR(1)
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.SH "COPYRIGHT"
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.br
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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
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.br
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.PP
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All rights reserved\&. On Debian\-based systems, please consult
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/usr/share/doc/primer3/copyright
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to read the licence of oligotm\&.
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.PP
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This manual page was written by Charles Plessy <plessy@debian\&.org> for the
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Debian(TM)
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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\&.
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.sp
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