Freiburg RNA Tools
SECISDesign - Results
SECISDesign 1310125

Input and runtime details for job 1310125 (precomputed example)

Original 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
?Processing 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 )

The job description you specified

Insert SECIS in MsrB


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 

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using SECISDesign please cite :

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