Input, Constraints, and Output

The usage, input, constraints-specifications and output are analogous to locarna; please refer to the help or man page of locarna for explanations and examples.

Scoring parameters:

-i, --indel=<score>(-150)

Indel score. Score contribution of each single base insertion or deletion. Indel opening score and indel score define the affine scoring of gaps.

-i, --indel-loop=<score>(-300)

Score for insertions and deletions of loops per base

--indel-opening=<score>(-750)

Indel opening score. Score contribution of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps.

--indel-opening-loop=<score>(-900)

Opening score for insertions and deletions of loops

--ribosum-file=<f>(RIBOSUM85_60)

File specifying the Ribosum base and base-pair similarities. [default: use RIBOSUM85_60 without requiring a Ribosum file.]

--use-ribosum=<bool>(true)

Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter.

-m, --match=<score>(50)

Set score contribution of a base match (unless ribosum scoring).

-M, --mismatch=<score>(0)

Set score contribution of a base mismatch (unless ribosum scoring).

--unpaired-penalty=<score>(0)

Penalty for unpaired bases

-s, --struct-weight=<score>(200)

Maximal weight of 1/2 arc match. Balances structure vs. sequence score contributions.

-e, --exp-prob=<prob>

Expected base pair probability. Used as background probability for base pair scoring [default: calculated from sequence length].

-t, --tau=<factor>(100)

Tau factor. Factor for contribution of sequence similarity in an arc match (in percent). tau=0 does not penalize any sequence information including compensatory mutations at arc matches, while tau=100 scores sequence similarity at ends of base matches (if a scoring matrix like ribosum is used, this adds the contributions for base pair match from the matrix). [default tau=0!]

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

Score contribution per exclusion in structure local alignment. Set to zero for unrestricted structure locality.

--stacking

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

--new-stacking

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

Partition function representation (for sequence envelopes):

--extended-pf

Use extended precision for the computation of sequence envelopes. This enables handling significantly larger instances. [default]

--quad-pf

Use quad precision for partition function values. Even more precision than extended pf, but usually much slower (overrides extended-pf).

Controlling_output:

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

Width of alignment output.

--clustal=<file>

Write alignment in ClustalW (aln) format to given file.

--stockholm=<file>

Write alignment Stockholm format to given file.

--pp=<file>

Write alignment in PP format to given file.

--alifold-consensus-dp

Compute consensus dot plot by alifold (warning: this may fail for long sequences).

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

Type of consensus structures written to screen and stockholm output [alifold|mea|none] (default: none).

--consensus-gamma=<float>(1.0)

Base pair weight for mea consensus computation. For MEA, base pairs are scored by their pair probability times 2 gamma; unpaired bases, by their unpaired probability.

-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.

--special-gap-symbols

Special distinct gap symbols for loop gaps or gaps caused by sparsification

--stopwatch

Print run time informations.

Heuristics for speed accuracy trade off:

-p, --min-prob=<prob>(0.001)

Minimal probability. Only base pairs of at least this probability are taken into account.

--prob-unpaired-in-loop-threshold=<threshold>(0.00005)

Threshold for prob_unpaired_in_loop

--prob-basepair-in-loop-threshold=<threshold>(0.0001)

Threshold for prob_basepair_in_loop

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

Maximal ratio of #base pairs divided by sequence length. This serves as a second filter on the "significant" base pairs. [default: 0.0 = no effect].

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

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

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

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

-D, --max-diff-am=<diff>(-1)

Maximal difference for sizes of matched arcs. [-1=off]

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

Maximal difference for positions of alignment traces (and aligned bases). [-1=off]

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

Maximal difference for positions of alignment traces at arc match ends. [-1=off]

--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=AMPERSAND)

--max-diff-relax

Relax deviation constraints in multiple aligmnent

--min-trace-probability=<probability>(1e-5)

Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) [default=1e-4].

MEA score:

--mea-alignment

Perform maximum expected accuracy alignment (instead of using the default similarity scoring).

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

Select method for computing sequence-based base match probablities (to be used for mea-type alignment scores). Methods: 1=probcons-style from HMM, 2=probalign-style from PFs, 3=from PFs, local

--probcons-file=<file>

Read parameters for probcons-like calculation of match probabilities from probcons parameter file.

--temperature-alipf=<int>(300)

Temperature for the /sequence alignment/ partition functions used by the probcons-like sequence-based match/trace probability computation (this temperature is different from the 'physical' temperature of RNA folding!).

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

Structure weight in PF computations (for the computation of sequence-based match probabilties from partition functions).

--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

Disallow lonely pairs in prediction and alignment.

--maxBPspan=<span>(-1)

Limit maximum base pair span [default=off].

--relaxed-anchors

Use relaxed semantics of anchor constraints [default=strict semantics].

Input files:

The tool is called with two input files <Input 1> and <Input 2>, which specify the two input sequences or input alignments. Different input formats (Fasta, Clustal, Stockholm, LocARNA PP, ViennaRNA postscript dotplots) are accepted and automatically recognized (by file content); the two input files can be in different formats. Extended variants of the Clustal and Stockholm formats enable specifying anchor and structure constraints.