Freiburg RNA Tools
SECISDesign - Results
BIF
IFF
SECISDesign 9176855

Input and runtime details for job 9176855 (precomputed example)

Original Protein Sequence

? Protein sequenceMSFCSFFGGEVFQNHFEPGVYVCAKCSYELFSSHSKYAHSSPWPAFTETIHPDSVTKCPEKNRPEALKVSCGKCGNGLGHEFLNDGPKRGQSRFCIFSSSLKFVPKGKEAAASQGH

SECIS Design Constraints

? Position of Selenocystein in Protein95
? Amino Acids to Conserve97 F 98 S T
? SECIS-Element Define your own SECIS element
? Custom structure[,[[[[[{[[/((.((((....))))))\]]}]]]]]]....
? Custom sequenceNNNNNNNNNNNSSUWSCAGGUCUGSWSSNNNNNNNNNNNNNN

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 9176855 (server version 4.0.0)

?Job Submitted & Queued@ Thu Jun 18 18:25:52 CEST 2015
?Processing Started@ Thu Jun 18 18:26:07 CEST 2015
?SECISDesign Finished & Post-Processing@ Thu Jun 18 18:26:36 CEST 2015
?Job Completed@ Thu Jun 18 18:26:37 CEST 2015
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=9176855&toolName=SECISDesign ( 30 days expiry )

The job description you specified

Custom SECIS in MsrB

Output

download full results [zip] [txt]

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

Wanted Structure:
[,[[[[[{[[/((.((((....))))))\]]}]]]]]]....

NNNNNNNNNNNSSUWSCAGGUCUGSWSSNNNNNNNNNNNNNN
Prob.:
mRNA-Sequence without optimizing the stability of the structure:
AUUUUCUCUUCGCUACCAGGUCUGGUGCCAAAAGGAAAAGAA
..(((((.((.((.((((....)))))).)).))))).....
.((((((.((.((.((((....)))))).)).))))))....

(0.04)
(0.19)
mRNA-Sequence after optimizing the stability of the structure:
AAGUUCUCUUCGCUAGCAGGUCUGCUGCCAAAAGGACAAGAA
..(((((.((.((.((((....)))))).)).))))).....

(0.58)


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