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>


This document was created by man2html, using the manual pages.
Time: 18:35:31 GMT, January 19, 2004