ensemble-ext / ensemble-ext-same

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Name

ensemble-ext, ensemble-ext-same - compute extinction of an ensemble of species

Synopsis

ensemble-ext [OPTION]... PREFIX1 PREFIX2
ensemble-ext-same [OPTION]... PREFIX

Description

ensemble-ext computes the extinction of a two-sequence ensemble. The input to ensemble-ext consists of the outputs of running hybrid or hybrid-ss on each species, as well as the output of running concentration on the ensemble. ensemble-ext writes PREFIX1-PREFIX2.ens.ext which containts the extinction of the ensemble at each temperature. It also writes PREFIX1-PREFIX2.ens.TmExt1 and PREFIX1-PREFIX2.ens.TmExt2, which contain the inflection and halfway points of the extinction curve. Both are approximations of the melting temperature; the latter is preferred. The file PREFIX1-PREFIX2.ens.MaxExt contains the maximum possible extinction, i.e. the extinction if all bases were unpaired.

ensemble-ext-same operates in the same manner on a one-sequence ensemble, using the output from concentration-same.

It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl and ensemble-dg and ensemble-ext instead of running ensemble-ext directly.

Options

-n, --NA=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-p, --points=number
use number points on either side of each point when performing numerical differentiation to determine the inflection point. Default is 1.
-x, --exclude=A|B|AA|BB
excludes the specified species from consideration. May be used more than once, to exclude multiple species.
-H, --enthalpy=value
assigns value kcal/mol of enthalpy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --entropy.
-S, --entropy=value
assigns value cal/mol/K of entropy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --enthalpy.
-o, --output=prefix
names output files with prefix.

Obscure Options

--single
only sum extinctions for each nucelotide, rather than for each dinucleotide.

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