# RNAPDIST

Vienna RNA (l) Return to Main Contents

## NAME

RNApdist - calculate distances between thermodynamic RNA secondary
structures ensembles
## SYNOPSIS

**RNApdist [-Xp|m|f|c] [-B [file]] [-T temp] [-4] [-d]
[-noGU] [-noCloseGU] [-e e_set] [-P paramfile]
[-nsp pairs]**
## DESCRIPTION

*RNApdist* reads RNA sequences from stdin and calculates
structure distances between the thermodynamic ensembles of their
secondary structures. To do this the partition function and matrix
of base pairing probabilities is computed for each sequence. The
probability matrix is then condensed into a vector holding for each
base the probabilities of being unpaired, paired upstream, or
paired downstream, respectively. These profiles are compared by a
standard alignment algorithm.
The base pair probabilities are also saved as postscript "dot
plots" (as in RNAfold) in the files "name_dp.ps", where name is the
name of the sequence, or a number if unnamed.

## OPTIONS

**-Xp**
- compare the structures pairwise (p), that is first with 2nd,
third with 4th etc. This is the default.
**-Xm**
- calculate the distance matrix between all structures. The
output is formatted as a lower triangle matrix.
**-Xf**
- compare each structure to the first one.
**-Xc**
- compare continuously, that is i-th with (i+1)th structure.
**-B [***<file>*]
- Print an "alignment" with gaps of the profiles, using the
following symbols:

( ) essentially upstream (downstream) paired bases

{ } weakly upstream (downstream) paired bases

| strongly paired bases without preference

, weakly paired bases without preference

. essentially unpaired bases.

The aligned structures are written to *<file>*, if
specified. Otherwise output is written to stdout, unless the -Xm
option is set in which case "backtrack.file" is used.

The **-T**, **-d**, **-4**, **-noGU**,
**-noCloseGU**, **-e**, **-P**, **-nsp**, options work
as in RNAfold.

## REFERENCES

Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993) RNA
multi-structure landscapes, Euro Biophys J:22,13-24
## VERSION

This man page documents version 1.8.5 Vienna RNA Package.
## AUTHORS

Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer.
## BUGS

We hoped you wouldn't find them.

Comments should be sent to rna@tbi.univie.ac.at

This document was created by man2html,
using the manual pages.

Time: 07:19:16 GMT, February 23, 2011