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Input and runtime details for job 1310125 (precomputed example)
Original Protein Sequence
Protein sequence | MSFCSFFGGEVFQNHFEPGVYVCAKCSYELFSSHSKYAHSSPWPAFTETIHPDSVTKCPEKNRPEALKVSCGKCGNGLGHEFLNDGPKRGQSRFCIFSSSLKFVPKGKEAAASQGH |
SECIS Design Constraints
Position of Selenocystein in Protein | 95 | ||
Amino Acids to Conserve | 97 F 98 S T | ||
SECIS-Element | FdhF-std (optional) | ||
Custom structure | not provided | ||
Custom sequence | not provided |
Similarity Scoring
Similarity | BLOSUM62 | ||
Insertion Penalty | -10 | ||
Deletion Penalty | -5 |
RNAinverse (local search)
Search Strategy | Full Local Search | ||
Objective Function | mfe -> pf | ||
Valid Similarity Fraction | 0.7 | ||
Compared Similarity | Start Similarity | ||
Probabilities of Bases | all 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: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1310125&toolName=SECISDesign ( 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.
Output
mRNA Sequence with Structure and its Probability for the SECIS-Element region after UGA stop codon
Wanted Structure: | [,[[[[[{[[/((.((((....))))))\]]}]]]]]].... | 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 |
Job resubmission
usability assessment
When using SECISDesign please cite :
- Anke Busch, Sebastian Will, and Rolf Backofen
SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence
Bioinformatics, 2005, 21(15), 3312-3. - 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 SECISDesign version 1.0 (2009-10-13) using Turner99 energies