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Input and runtime details for job 0123863 (precomputed example)
General Parameters
Sequence Input in FASTA Format | [.fa] | ||
Structure Computation | minimum free energy structure (RNAfold, default) | ||
Scores | none |
Scoring Parameters
arc removing | 2 | ||
arc breaking | 1 | ||
arc mismatch | 2 | ||
base deletion | 1.5 | ||
base mismatch | 1.8 |
Job ID 0123863 (server version trunk)
Job Submitted & Queued | @ Fri Jan 07 20:14:03 CET 2022 | ||
MARNA Started | @ Fri Jan 07 20:14:14 CET 2022 | ||
MARNA Finished & Post-Processing | @ Fri Jan 07 20:14:19 CET 2022 | ||
Job Completed | @ Fri Jan 07 20:14:19 CET 2022 |
DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=0123863&toolName=MARNA ( 30 days expiry )
Description of the job
Alignment of five different bacterial tRNAs including predefined structures.
Output
download full results [.zip]
Results
Input sequences :
>AB013372
GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGGGCGCG
(((((((..((((.........)))).((((((....).))))).....(((((.....)))))..))))))).
>AB013373
GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCU
(((((((..((((.......)))).((((((.....)))))).....(((((.......)))))))))))).
>AE000930
GGCCCGUAGCUCAGACUGGGAGAGCGCCGCCCUUGCAAGGCGGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA
(((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))..
>AB067577
GGGCUAUUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCCCUGGUUCAAGUCCAGGAUGGCCCA
((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
>AF034440
GUUGAUGUAGCUUAACCCAAAGCAAGGCACUGAAAAUGCCUAGAUGAGUCUCCCAACUCCAUAAACA
(((.(((..((((......)))).(((((.(....))))))....((((......))))))).))).
5 sequences found. Sequences without given structures have been assigned an ensemble of 3 highly probable structures.
Scores used :
base deletion (w_d) = 2
base mismatch (w_m) = 1
arc removing (w_r) = 2
arc breaking (w_b) = 1.5
arc mismatch (w_am)= 1.8Alignment :
AB013372 GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGGGCGCGA row with stars characterizes the ambigous assignment of multiple structures to a sequence.
AB013373 GCGGAAGUAGUUCAGU-GG-UAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCU
AE000930 -GGCCCGUAGCUCAGACUGGGAGAGCGCCGCCCUUGCAAGGCGGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA
AB067577 GGGCUAUUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCCCUGGUUCAAGUCCAGGAUGGCCCA
AF034440 GUUGAUGUAGCUUAACC---CAAAGCAAGGCACUGAAAAUGCCUAGAUGAGUCUCCCAACUCCAUAA----ACA
Seq gNgcNNgUAGcUcAgNNggNuAgAgCgcNNcccUgNNaAggNNgaGgucNcggguuCaANUCCNgNNNggcNCa
AB013372 (((((((..((((.........)))).((((((....).))))).....(((((.....)))))..))))))).
AB013373 (((((((..((((...-..-..)))).((((((.....)))))).....(((((.......)))))))))))).
AE000930 -(((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))..
AB067577 ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
AF034440 (((.(((..((((....---..)))).(((((.(....))))))....((((......))))))).)----)).
Str(50%) ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
Str(60%) ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
Str(70%) ((((((...((((.........)))).(((((.......))))).......................)))))).
Str(80%) ((((((...((((.........)))).(((((.......))))).......................)))))).
Str(90%) .(.......((((.........)))).(((((.......)))))...........................)..
Str(100%) .(.......((((.........)))).(((((.......)))))...........................)..
The consensus sequence(in blue) is successively constructed column by column. A capital letter indicates
the full conservation of a nucleotide. A lowercase letter indicates a nucleotide conservation in at least
50% of all sequences. The consensus structures reflect the conservation of base-pairs in per cent
occurring in all structures.
Job resubmission
usability assessment
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