| NTTHAL(1) | Primer3 User Manuals | NTTHAL(1) |
ntthal - Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
ntthal is analogous to ntdpal. Between two sequences, ntthal finds alignment/sec structure, that has the highest melting temperature. Ntthal is based on nearest-neighbor thermodynamical approach.
ntthal OPTIONS oligo
-mv monovalent_conc - concentration of monovalent cations in mM, by default 50 mM
-dv divalent_conc - concentration of divalent cations in mM, by default 0 mM
-n dNTP_conc - concentration of deoxynycleotide triphosphate in mM, by default 0 mM
-d dna_conc - concentration of DNA strands in nM, by default 50 nM
-a mode - alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
-t temp - temperature at which duplex is calculated, by default 37C
-r - causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
-maxloop size - the maximum size of secondary structures loops.
-path <path> - the path to the thermodynamic parameter files
-s1 DNA_oligomer
-s2 DNA_oligomer
This manual page was created by Andreas Tille <tille@debian.org> using help2man for Debian but can be freely used for any other purpose
| December 2013 | 2.3.6 |