Freiburg RNA Tools
MARNA - Results
BIF
IFF
MARNA 0123863

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)
? Scoresnone

Scoring Parameters

? arc removing2
? arc breaking1
? arc mismatch2
? base deletion1.5
? base mismatch1.8

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: http://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)= 1.8

Alignment :

AB013372    GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGGGCGCG
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%) .(.......((((.........)))).(((((.......)))))...........................)..
A row with stars characterizes the ambigous assignment of multiple structures to a sequence.
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.

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When using MARNA please cite :

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