Freiburg RNA Tools
SECISDesign - Results
SECISDesign 1310125

Input and runtime details for job 1310125 (precomputed example)

Original Protein Sequence

? Protein sequence

SECIS Design Constraints

? Position of Selenocystein in Protein95
? Amino Acids to Conserve97 F 98 S T
? SECIS-Element FdhF-std (optional)
? Custom structurenot provided
? Custom sequencenot provided

Similarity Scoring

? SimilarityBLOSUM62
? Insertion Penalty-10
? Deletion Penalty-5

RNAinverse (local search)

? Search Strategy Full Local Search
? Objective Function mfe -> pf
? Valid Similarity Fraction0.7
? Compared SimilarityStart Similarity
? Probabilities of Basesall equal

Job ID 1310125 (server version 4.0.0)

?Job Submitted & Queued@ Thu Jun 18 18:25:24 CEST 2015
?SECISDesign Started@ Thu Jun 18 18:25:37 CEST 2015
?SECISDesign Finished & Post-Processing@ Thu Jun 18 18:26:05 CEST 2015
?Job Completed@ Thu Jun 18 18:26:06 CEST 2015
 DIRECT ACCESS: ( 30 days expiry )

Description of the job

Insert SECIS in MsrB

Insert SECIS to mammalian methionine sulfoxide reductase B (MsrB). See help page for an explanation of the output.


download full results [zip] [txt]

mRNA Sequence with Structure and its Probability for the SECIS-Element region after UGA stop codon

Wanted Structure:
mRNA-Sequence without optimizing the stability of the structure:

mRNA-Sequence after optimizing the stability of the structure:


Amino Acid Sequence after selenocystein insertion position

Original Sequence
(starting at pos. 96):
 I F S S S L K F V P K G K E 
Without optimizing the stability of the mRNA-structure:
 I F S S L P G L V P K G K E 
After optimizing the stability of the mRNA-structure:
 K F S S L A G L L P K G Q E 

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When using SECISDesign please cite :

Results are computed with SECISDesign version 1.0 (2009-10-13) using Turner99 energies