Input and runtime details for job 9176855 (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		Define your own SECIS element
	Custom structure		[,[[[[[{[[/((.((((....))))))\]]}]]]]]]....
	Custom sequence		NNNNNNNNNNNSSUWSCAGGUCUGSWSSNNNNNNNNNNNNNN

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 9176855 (server version 4.0.0)

	Job Submitted & Queued		@ Thu Jun 18 18:25:52 CEST 2015
	SECISDesign 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/RetrieveResults.jsp?jobID=9176855&toolName=SECISDesign ( 30 days expiry )

Description of the job

Custom SECIS in MsrB

Insert a custom SECIS (which is FdhF-std (optional)) to mammalian methionine sulfoxide reductase B (MsrB). See help page for an explanation of the output.

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

Job resubmission

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

usability assessment

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service.

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

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