Freiburg RNA Tools
MARNA - Help
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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 :

Results are computed with MARNA version compiled at 2010-07-29 linking Vienna RNA package 1.8.4

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 ().

?  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 a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

?  arc breaking

Score weight for breaking an arc. Please refer to the article.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

?  arc mismatch

Score weight for an arc mismatch. Please refer to the article.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

?  base deletion

Score weight for deleting a base. Please refer to the article.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

?  base mismatch

Score weight for a base mismatch. Please refer to the article.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1000.

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