https://github.com/s-will/carna

CARNA constraint-based alignment of RNAs
https://github.com/s-will/carna

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CARNA constraint-based alignment of RNAs

• Host: GitHub
• URL: https://github.com/s-will/carna
• Owner: s-will
• License: gpl-3.0
• Created: 2019-11-22T14:52:44.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2019-11-22T14:54:10.000Z (about 5 years ago)
• Last Synced: 2024-11-03T11:42:47.408Z (3 months ago)
• Language: TeX
• Size: 5.81 MB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: ChangeLog
  • License: COPYING
  • Authors: AUTHORS

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README

        
CARNA 1.2.8 (Constraint Alignment of RNA)

=======================================

SYNOPSIS

--------

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

------------

For *installation instructions*, see INSTALL.

CARNA HELP

----------

A tool for pairwise Alignment of RNA.

Usage: _inst/bin/carna  [] []

Scoring parameters:

    -m,--match=(50)            Match score

    -M,--mismatch=(0)          Mismatch score

    --ribosum-file=(RIBOSUM85_60)  Ribosum file

    --use-ribosum=(true)        Use ribosum scores

    -i,--indel=(-350)          Indel score

    --indel-opening=(-500)     Indel opening score

    -s,--struct-weight=(200)   Maximal weight of 1/2 arc match

    -e,--exp-prob=              Expected probability

    -t,--tau=(0)              Tau factor in percent

Controlling output:

    --gist                            Use gist for interactive/graphical search.

    -w,--width=(120)         Output width

    --clustal=                  Clustal output

    --pp=                       PP output

    --write-structure                 Write guidance structure in output

Heuristics for speed accuracy trade off:

    -p,--min-prob=(0.01)        Minimal probability

    --max-bps-length-ratio=(0.0) Maximal ratio of #base pairs divided by sequence length (default: no effect)

    -D,--max-diff-am=(-1)       Maximal difference for sizes of matched arcs

    -d,--max-diff=(-1)          Maximal difference for alignment cuts

    --max-diff-at-am=(-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=()              Anchor constraints sequence A.

    --anchorB=()              Anchor constraints sequence B.

    --ignore-constraints              Ignore constraints in pp-file

    --lb=                      Lower score bound

    --ub=                      Upper score bound

Controlling Gecode:

    --c_d=(1)               Recomputation distance

    --time-limit=(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:

                              Input file 1  ;; input files can be fasta, dotplot, pp, or aln files

                              Input file 2  ;; and can speficy structure and anchor constraints.