This is the command ntthal that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
ntthal - Provides Primer3's alignment functionality based on nearest-neighbor
thermodynamical approach
DESCRIPTION
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.
SYNOPSIS
ntthal OPTIONS oligo
OPTIONS
-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.
Default is 30 (this is maximum allowed length, currently).
-path <path> - the path to the thermodynamic parameter files
-s1 DNA_oligomer
-s2 DNA_oligomer
AUTHORS
This manual page was created by Andreas Tille <[email protected]> using help2man for Debian
but can be freely used for any other purpose
Use ntthal online using onworks.net services
