**Introduction**

Please note:

MARNA is not maintained anymore since 2005. For the task of multiple
sequence-structure RNA alignment the more advanced tool
LocARNA is
superseding MARNA (check fixed structure input in LocARNA help page).

MARNA is a multiple alignment of RNAs taking into consideration
both the primary sequence and the secondary structure.
It is based on pairwise comparisons using costs of edit operations.
The edit operations can be divided into edit operations on arcs and
edit operations on bases.
Additionally, MARNA predicts a consensus sequence as well as a consensus structure.
The source code is available at
http://www.bioinf.uni-freiburg.de/Software/MARNA/download/

# When using MARNA please cite :

- Sven Siebert and Rolf Backofen

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons

Bioinformatics 2005, Volume 21, Issue 16, 3352-3359

- Sven Siebert and Rolf Backofen

MARNA: A server for multiple alignment of RNAs

In Proc. of German Conference on Bioinformatics (GCB'03), pages 135-140, October 2003

- Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with MARNA version compiled at 2010-07-29 linking Vienna RNA package 1.8.4 and using T-Coffee 13.45.0

**Overview**

The following parameters are used to control the execution of MARNA

Furthermore, additional information is available

# General Parameters

## Sequence Input in FASTA Format

MARNA accepts input in form of a multiple FASTA file.
It consists of i) sequence names, ii) primary sequences and probably
iii) secondary structures (given in dot-bracket notation with a
tailing ' #FS'). Input can be given either as direct text input or
uploading a file. The max. sequence length should not exceed 500nt.
The number of sequences depends on sequence lengths. The total sum
of all sequence lengths is restricted to 10,000nt, e.g., you can
paste 20 sequences with lengths of 500nt each, or 100 sequences
with lengths of 100nt, each.

The parameter constraints are: The input has to be in valid FASTA format. The number of sequences has to be at least 2 and at most 30. Sequence lengths have to be in the range 1-1000. The allowed sequence alphabet is 'ACGUacgu'. Fixed structure can be given in a single line with tailing '#FS' using the brace pairs ().

Defaults to ()

## Structure Computation

If you don't specify any structure to a sequence, then you can choose whether this sequence should adopt the minimum free energy structure, an ensemble of shaped structures (using RNAshapes) or an ensemble of highly probable structures (using RNAsubopt, current number of structures is 3)

## Scores

MARNA allows you to tune your individual scoring set. For simplicity, you can attach importance to sequential parameters, to structural parameters, to a mixture of both (default) or to its individual parameter set. For further details on the scoring please refer to the article.

# Scoring Parameters

## arc removing

Score weight for removing an arc. Please refer to the article.

The parameter constraints are: Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

Defaults to (2)

## arc breaking

Score weight for breaking an arc. Please refer to the article.

The parameter constraints are: Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

Defaults to (1)

## arc mismatch

Score weight for an arc mismatch. Please refer to the article.

The parameter constraints are: Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

Defaults to (2)

## base deletion

Score weight for deleting a base. Please refer to the article.

The parameter constraints are: Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

Defaults to (1.5)

## base mismatch

Score weight for a base mismatch. Please refer to the article.

The parameter constraints are: Input value has to be parsable as Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

Defaults to (1.8)

# Input Examples

## tRNA alignment

Alignment of five different bacterial tRNAs including predefined structures.

The

example's result can be directly accessed

here
# List of Changes

- 3.3.1 : FASTA input: bugfix structure constraint parsing