CARNA 1.2.8 (Constraint Alignment of RNA)
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SYNOPSIS
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CARNA aligns multiple RNAs without any restrictions on the base
pairing dependencies in the RNA structure ensembles. Typical RNA
alignment tools (like FoldAlign or LocARNA) consider only non-crossing
interactions or predict non-crossing structures simultaneously to
finding the optimal alignments. In contrast, CARNA considers all
interactions in the input at the same time and without
restrictions. This allows finding optimal alignments that take
pseudoknots and even structural alternatives into account. While
typical RNA analysis tools have to limit base pairing interactions for
reasons of computational complexity, CARNA tackles the problem by
advanced constraint programming methods.
INSTALLATION
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For *installation instructions*, see INSTALL.
CARNA HELP
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A tool for pairwise Alignment of RNA.
Usage: _inst/bin/carna <options> [<file 1>] [<file 2>]
Scoring parameters:
-m,--match=<score>(50) Match score
-M,--mismatch=<score>(0) Mismatch score
--ribosum-file=<f>(RIBOSUM85_60) Ribosum file
--use-ribosum=<bool>(true) Use ribosum scores
-i,--indel=<score>(-350) Indel score
--indel-opening=<score>(-500) Indel opening score
-s,--struct-weight=<score>(200) Maximal weight of 1/2 arc match
-e,--exp-prob=<prob> Expected probability
-t,--tau=<factor>(0) Tau factor in percent
Controlling output:
--gist Use gist for interactive/graphical search.
-w,--width=<columns>(120) Output width
--clustal=<file> Clustal output
--pp=<file> PP output
--write-structure Write guidance structure in output
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)
-D,--max-diff-am=<diff>(-1) Maximal difference for sizes of matched arcs
-d,--max-diff=<diff>(-1) Maximal difference for alignment cuts
--max-diff-at-am=<diff>(-1) Maximal difference for alignment traces, only at arc match positions
Constraints:
--noLP No lonely pairs (only used when predicing ensemble porobabilities and for compatibility with locarna; otherwise no effect)
--anchorA=<string>() Anchor constraints sequence A.
--anchorB=<string>() Anchor constraints sequence B.
--ignore-constraints Ignore constraints in pp-file
--lb=<score> Lower score bound
--ub=<score> Upper score bound
Controlling Gecode:
--c_d=<distance>(1) Recomputation distance
--time-limit=<time>(300000) Time limit in ms (always search first solution; turn off by 0).
Standard options:
-h,--help This help
-V,--version Version info
-v,--verbose Verbose
RNA sequences and pair probabilities:
<file 1> Input file 1 ;; input files can be fasta, dotplot, pp, or aln files
<file 2> Input file 2 ;; and can speficy structure and anchor constraints.