Input

Input consists of two sequences or alignments, which are specified in fasta, clustal, stockholm, or LocARNA pp format.

Optionally, one can specify structure and anchor constraints in these input files.

Output

The program enumerates exactly matching local substructures (exact pattern matches = EPMs) and optionally chains them. It returns lists of chained and unchained matches, visualizations of the results and anchor constraints for alignment.

Scoring parameters:

--no-stacking

Do not use stacking terms (otherwise needs stacking probs by RNAfold -p2)

--alpha_1=<factor>(1)

Multiplier for sequential score

--alpha_2=<factor>(5)

Multiplier for structural score

--alpha_3=<factor>(5)

Multiplier for stacking score, 0 means no stacking contribution

--struct-mismatch-score=<score>(-10)

Score for a structural mismatch (nucleotide mismatch in an arcmatch)

Heuristics for speed accuracy trade off:

-p, --min-prob=<prob>(0.01)

Minimal probability

--max-bps-length-ratio=<factor>(0.0)

Maximal ratio of #base pairs divided by sequence length (default: no effect)

--max-uil-length-ratio=<factor>(0.0)

Maximal ratio of #unpaired bases in loops divided by sequence length (default: no effect)

--max-bpil-length-ratio=<factor>(0.0)

Maximal ratio of #base pairs in loops divided by loop length (default: no effect)

-D, --max-diff-am=<diff>(30)

Maximal difference for sizes of matched arcs

-d, --max-diff=<diff>(-1)

Maximal difference for alignment traces

--max-diff-at-am=<diff>(-1)

Maximal difference for alignment traces, only at arc match positions

--prob_unpaired_in_loop_threshold=<prob>(0.01)

Threshold for prob_unpaired_in_\ loop

--prob_basepair_in_loop_threshold=<prob>(0.01)

Threshold for prob_basepair_in_\ loop

Output:

-p, --out-min-prob=<prob>(0.0005)

Minimal probability for output (min-prob overrides if smaller)

--output-ps

Output best EPM chain as colored postscript

-a, --PS_fileA=<file>()

Postscript output file for sequence A

-b, --PS_fileB=<file>()

Postscript output file for sequence B

-o, --output-locarna=<file>()

Fasta file with anchor constraints for locarna

--output-anchor-pp=<fileroot>()

PP files <fileroot>_A.pp and <fileroot>_B.pp, merging input PPs and anchor constraints from chaining

--output-clustal=<file>()

Write file with chain as alignment in clustalw format

--output-epm-list=<file>()

A list of all found epms

--output-chained-epm-list=<file>()

A list of all EPMs that are present in the chain

--inexact-struct-match

Allow inexact structure matches

--add-filter

Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)

--no-chaining

Do not use the chaining algorithm to find best overall chain

Suboptimal traceback:

--subopt

Use the suboptimal traceback

--diff-to-opt-score=<threshold>(-1)

Threshold for suboptimal traceback

--min-score=<score>(90)

Minimal score of a traced EPM

--number-of-EPMs=<threshold>(100)

Maximal number of EPMs for the suboptimal traceback

Constraints:

--noLP

use --noLP option for folding

--maxBPspan=<span>(-1)

Limit maximum base pair span (default=off)

--relaxed-anchors

Relax anchor constraints (default=off)

Miscellaneous:

--stopwatch

Print run time information.

Input files:

The two input files <Input 1> and <Input 2> specify the input sequences in various, automatically detected formats. Accepted formats are: Fasta, Clustal, Stockholm LocARNA PP, ViennaRNA postscript dotplot. Unless in-loop

probabilities are provided (only possible in LocARNA PP),

base pair

probabilities are computed by partition function folding.

Clustal, Stockholm, and PP input can contain constraints.