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diff --git a/academic/primer3/man1/ntthal.1 b/academic/primer3/man1/ntthal.1 new file mode 100644 index 0000000000000..e3e5e8888a08f --- /dev/null +++ b/academic/primer3/man1/ntthal.1 @@ -0,0 +1,40 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. +.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals" +.SH NAME +ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach +.SH DESCRIPTION +\fBntthal\fR is analogous to \fBntdpal\fR. Between two sequences, \fBntthal\fR finds +alignment/sec structure, that has the highest melting +temperature. Ntthal is based on nearest-neighbor thermodynamical +approach. +.SH SYNOPSIS +.B ntthal +\fIOPTIONS\fR oligo +.SH OPTIONS +\fB\-mv\fR monovalent_conc \- concentration of monovalent cations in mM, by default 50 mM +.PP +\fB\-dv\fR divalent_conc \- concentration of divalent cations in mM, by default 0 mM +.PP +\fB\-n\fR dNTP_conc \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM +.PP +\fB\-d\fR dna_conc \- concentration of DNA strands in nM, by default 50 nM +.PP +\fB\-a\fR mode \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex) +.PP +\fB\-t\fR temp \- temperature at which duplex is calculated, by default 37C +.PP +\fB\-r\fR \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed +.PP +\fB\-maxloop\fR size \- the maximum size of secondary structures loops. +.IP +Default is 30 (this is maximum allowed length, currently). +.PP +\fB\-path\fR <path> \- the path to the thermodynamic parameter files +.PP +\fB\-s1\fR DNA_oligomer +.PP +\fB\-s2\fR DNA_oligomer +.SH AUTHORS +This manual page was created by Andreas Tille <tille@debian.org> using help2man +for Debian but can be freely used for any other purpose + |