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RNAhybrid - Manual
from the man pageRNAhybrid is a tool for finding minimum free energy hybridisations of a long (target) and a short (query) RNA. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting parts of the long one. The tool is primarily meant as a means for microRNA target prediction.
The web form of the online version of RNAhybrid offers a various number of options (shown below) to run RNAhyrbid.
target RNA :
Each of the target sequences in target_file is subjectto
hybridisation with each of the queries (which either are from the
query_file or is the one query given on command line; see -q
below). The sequences in the target_file have to be in FASTA
format, ie. one line starting with a > and directly followed
by a name, then one or more following lines with the sequence
itself. Each individual sequence line must not have more than
1000 characters. If no -t is given, either the last argument (if
a -q is given) or the second last argument (if no -q is given) to
RNAhybrid is taken as a target.
query RNA :
see target RNA description
hit per target (-b) :
Maximal number of hits to show. hit_number hits with increasing
minimum free energy (reminder: larger energies are worse) are
shown, unless the -e option is usedand the energy cut-off has
been exceeded (see -e option below) or there are no more hits.
Hits may only overlap at dangling bases (5' or 3' unpaired end of
target).
compact output (-c) (optional) :
Produce compact output. For each target/query pair one line of
output is generated. Each line is a colon (:) separated list of
the following fields: target name, query name, minimum free
energy, position in target, alignment line 1, line 2, line 3,
line 4.
helix constraint (-f) (optional) :
Forces all structures to have a helix from position from to
position to with respect to the query. The first base has
position 1.
maximal internal loop size (-u) (optional) :
The maximally allowed number of unpaired nucleotides in either
side of an internal loop.
maximal bulge loop size (-v) (optional) :
The maximally allowed number of unpaired nucleotides in either
side of an internal loop.
Hits with increasing minimum free energy (reminder: larger energies are worse) less than or equal to energy_cutoff are shown, unless the -b option is used and the number of already reported hits has reached the maximal hit_number (see -b option above). Hits may only overlap at dangling bases (5' or 3' unpaired end of target).
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