LOCARNA(1)

NAME
LocARNA - manual page for LocARNA 1.9.0

DESCRIPTION
locarna - a tool for pairwise (global and local) alignment of RNA.

USAGE: ../../src/locarna [-h,--help] [--galaxy-xml] [-V,--version] [-v,--verbose] [-q,--quiet] -m,--match=<score> -M,--mismatch=<score> --ribosum-file=<f> --use-ribosum=<bool> -i,--indel=<score> --indel-opening=<score> --unpaired_penalty=<score> -s,--struct-weight=<score> [-e,--exp-prob=<prob>] -t,--tau=<factor> -E,--exclusion=<score> [--stacking] [--new-stacking] [--struct-local=<bool>] [--sequ-local=<bool>] --free-endgaps=<spec> [--normalized=<L>] [--penalized=<PP>] -w,--width=<columns> [--clustal=<file>] [--stockholm=<file>] [--pp=<file>] [--alifold-consensus-dp] --consensus-structure=<type> [-L,--local-output] [--local-file-output] [-P,--pos-output] [--write-structure] [--score-components] [--stopwatch] -p,--min-prob=<prob> --max-bps-length-ratio=<factor> -D,--max-diff-am=<diff> -d,--max-diff=<diff> --max-diff-at-am=<diff> --max-diff-aln=<aln file> --max-diff-pw-aln=<alignment> [--max-diff-relax] -a,--min-am-prob=<amprob> -b,--min-bm-prob=<bmprob> [--kbest=<k>] [--better=<t>] [--mea-alignment] [--probcons-file=<file>] --match-prob-method=<int> --temperature=<int> --pf-struct-weight=<weight> [--mea-gapcost] --mea-alpha=<weight> --mea-beta=<weight> --mea-gamma=<weight> --probability-scale=<scale> [--write-match-probs=<file>] [--read-match-probs=<file>] [--write-arcmatch-scores=<file>] [--read-arcmatch-scores=<file>] [--read-arcmatch-probs=<file>] [--noLP] --maxBPspan=<span> [<input1>] [<input2>]

OPTIONS
cmd_only:

-h,--help

    Help

--galaxy-xml

    Galaxy xml wrapper

-V,--version

    Version info

-v,--verbose

    Verbose

-q,--quiet

    Quiet

  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

--unpaired_penalty=<score>(0)

    Penalty for unpaired bases

-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

-E,--exclusion=<score>(0)

    Exclusion weight

--stacking

    Use stacking terms (requires stack-probs by RNAfold -p2)

--new-stacking

    Use new stacking terms (requires stack-probs by RNAfold -p2)

  Locality_type:

--struct-local=<bool>(false)

    Structure local

--sequ-local=<bool>(false)

    Sequence local

--free-endgaps=<spec>(----)

    String of four +/- symbols, allowing/disallowing free end gaps at the four sequence ends in the order left end of first sequence, right end of first sequence, left end of second sequence, right end of second sequence.

--normalized=<L>(0)

    Normalized local alignment with parameter L

--penalized=<PP>(0)

    Penalized local alignment with penalty PP

  Controlling_output:

-w,--width=<columns>(120)

    Output width

--clustal=<file>

    ClustalW (aln) output

--stockholm=<file>

    Stockholm output

--pp=<file>

    PP output

--alifold-consensus-dp

    Compute consensus dot plot by alifold

--consensus-structure=<type>(alifold)

    Type of consensus structures written to screen and stockholm output [alifold|mea|none]

-L,--local-output

    Output only local sub-alignment (to std out)

--local-file-output

    Write only local sub-alignment to output files

-P,--pos-output

    Output only local sub-alignment positions

--write-structure

    Write guidance structure in output

--score-components

    Output components of the score (experimental)

--stopwatch

    Print run time information.

  Heuristics for speed accuracy trade off:

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

    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 traces

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

    Maximal difference for alignment traces, only at arc match positions

--max-diff-aln=<aln file>()

    Maximal difference relative to given alignment (file in clustalw format)

--max-diff-pw-aln=<alignment>()

    Maximal difference relative to given alignment (string, delim=AMPERSA\ ND)

--max-diff-relax

    Relax deviation constraints in multiple aligmnent

-a,--min-am-prob=<amprob>(0.0005)

    Minimal Arc-match probability

-b,--min-bm-prob=<bmprob>(0.0005)

    Minimal Base-match probability

  Special sauce options:

--kbest=<k>(-1)

    Enumerate k-best alignments

--better=<t>(-1000000)

    Enumerate alignments better threshold t

  MEA_score controlling options:

--mea-alignment

    Do MEA alignment

--probcons-file=<file>

    Probcons parameter file

--match-prob-method=<int>(0)

    Method for computation of match probs

--temperature=<int>(150)

    Temperature for PF-computation

--pf-struct-weight=<weight>(200)

    Structure weight in PF-computation

--mea-gapcost

    Use gap cost in mea alignment

--mea-alpha=<weight>(0)

    Weight alpha for MEA

--mea-beta=<weight>(200)

    Weight beta for MEA

--mea-gamma=<weight>(100)

    Weight gamma for MEA

--probability-scale=<scale>(10000)

    Scale for probabilities/resolution of mea score

--write-match-probs=<file>

    Write match probs to file (don't align!)

--read-match-probs=<file>

    Read match probabilities from file

--write-arcmatch-scores=<file>

    Write arcmatch scores (don't align!)

--read-arcmatch-scores=<file>

    Read arcmatch scores

--read-arcmatch-probs=<file>

    Read arcmatch probabilities (weighted by factor mea_beta/100)

  Constraints:

--noLP

    No lonely pairs

--maxBPspan=<span>(-1)

    Limit maximum base pair span (default=off)

  Input_files RNA sequences and pair probabilities:

    <input1>

    Input file 1

    <input2>

    Input file 2

REPORTING BUGS
Report bugs to <will (at) informatik.uni-freiburg.de>.