hxmatch
NAME
hxmatch
- prediction of RNA consensus structure including pseudoknots
SYNTAX
hxmatch [-len length] [-T thresh] [-N] [-A alifile] [-W pairsfile]
DESCRIPTION
hxmatch
reads an alignment file from stdin and calculates the
consensus bi-secondary structure.
The multiple sequence alignment must be contained in a single file in
ClustalW format. In particular, the first line of the alignment file must
begin with the word CLUSTAL.
hxmatch
produces a file containing the consensus structure of the alignment in
bracket notation. For each predicted base
pair i-j there is a line of the form
i j wt xx col rm comp g-g mut
written to stdout, the abbreviations are as follows:
- wt
-
weight of base pair i-j
- xx
-
2, if the base pair is the beginning of a helix
1, if the base pair is in the middle of a helix
3, if the base pair is the end of a helix
- col
-
U, if the base pair belongs to the part of the structure drawn
in the upper half plane (secondary structure)
L, if the base pair belongs to the part of the structure drawn
in the lower half plane (pseudoknots)
- rm
-
the number of rematching events for base pair i-j
during the run of the MWM algorithm
- comp
-
the number of sequences compatible with base pair i-j
- g-g
-
the number of sequences containing gaps at positions i-j
- mut
-
the number of different pairing combinations at position
i-j of the alignment
OPTIONS
- -A file
-
incorporate RNAalifold-results: all base pairs predicted by RNAalifold
file has to be the dot plot PostScript file (alirna.ps)
generated by RNAalifold
- -AP file
-
incorporate RNAalifold-results: only base pairs with base pairing
probability higher than 90 %
file has to be the output file (alifold.out)
generated by RNAalifold -p
- -help
-
Output help information and exit.
- -len length
-
set lower-bond of helix-length to length.
(length has to be an integer)
(default: 3)
- -N
-
use the greedy algorithm instead of MWM
(default: MWM)
- -T thresh
-
use threshold thresh*(pi*);
(thresh has to be an integer, pi*=25 kcal/mol)
(default: 1)
- -W pairsfile
-
incorporate weighted base pairs
pairsfile has the following format:
for each base pair there is a line of the form "i j weight"
where i<j, and i and j refer to the numbering in the alignment;
weight is the additional weight of base pair i-j in kcal/mol,
weight has to be an integer
EXAMPLES
To run this program the standard way type:
hxmatch -A tm8_alirna.ps < tm8.aln
REFERENCES
hxmatch uses the implementation of the MWM algorithm by Edward Roth-
berg, available at
ftp://dimacs.rutgers.edu/pub/netflow/matching/weighted/solver-1/
AUTHORS
Christina Witwer <xtina@tbi.univie.ac.at>
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Time: 18:35:31 GMT, January 19, 2004