RNAPALN
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NAME
RNApaln - RNA alignment based on sequence base pairing propensities
SYNOPSIS
RNApaln [-Xp|m|f|c] [-B [file]] [--gapo open] [--gape ext]
[--seqw w] [--endgaps] [-T temp] [-4] [-d] [-noGU]
[-noCloseGU] [-e e_set] [-P paramfile]
[-nsp pairs]
DESCRIPTION
RNApaln Uses string-alignment techniques to perform fast
pairwise structural alignments of RNAs. Similar to RNApdist
secondary structure is incorporated in an approximate manner by
computing base pair probabilities, which are then reduced to a
vector holding the probability that a base is paired upstream,
downstream, or remains unpaired. Such pair propsensity vectors can
then be compared using standard alignment algorithms. In contrast
to RNApdist, RNApaln performs similarity (instead of distance)
alignments, considers both sequence and structure information, and
uses affine (rather than linear) gap costs. RNApaln can perform
semi-local alignments by using free end gaps, a true local
alignment mode is planned.
The same approach has since been used in the StraL program from
Gerhard Steeger's group. Since StraL has optimized parameters and a
multiple alignment mode, it be be currently the better option.
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.
- --gapo open
- Set the gap open penalty to open --gape
ext Set the gap extension penalty to ext
--seqw w Set the weight of sequence (compared to
structure) in the scoring function. --endgaps Use free
end-gaps.
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,
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Time: 07:19:16 GMT, February 23, 2011