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40 lines
1.6 KiB
Groff
40 lines
1.6 KiB
Groff
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
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.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals"
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.SH NAME
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ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
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.SH DESCRIPTION
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\fBntthal\fR is analogous to \fBntdpal\fR. Between two sequences, \fBntthal\fR finds
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alignment/sec structure, that has the highest melting
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temperature. Ntthal is based on nearest-neighbor thermodynamical
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approach.
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.SH SYNOPSIS
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.B ntthal
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\fIOPTIONS\fR oligo
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.SH OPTIONS
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\fB\-mv\fR monovalent_conc \- concentration of monovalent cations in mM, by default 50 mM
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.PP
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\fB\-dv\fR divalent_conc \- concentration of divalent cations in mM, by default 0 mM
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.PP
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\fB\-n\fR dNTP_conc \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM
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.PP
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\fB\-d\fR dna_conc \- concentration of DNA strands in nM, by default 50 nM
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.PP
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\fB\-a\fR mode \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
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.PP
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\fB\-t\fR temp \- temperature at which duplex is calculated, by default 37C
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.PP
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\fB\-r\fR \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
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.PP
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\fB\-maxloop\fR size \- the maximum size of secondary structures loops.
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.IP
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Default is 30 (this is maximum allowed length, currently).
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.PP
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\fB\-path\fR <path> \- the path to the thermodynamic parameter files
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.PP
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\fB\-s1\fR DNA_oligomer
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.PP
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\fB\-s2\fR DNA_oligomer
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.SH AUTHORS
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This manual page was created by Andreas Tille <tille@debian.org> using help2man
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for Debian but can be freely used for any other purpose
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