SECISDesign - Insert SECIS in mRNA

SECISDesign is a server for the design of SECIS-elements within the coding sequence of an mRNA with both structure and sequence constraints. This will trigger the insertion of a selenocystein at a preceding STOP codon. Furthermore, a certain similarity to the original protein sequence is kept. It can be used e.g. for recombinant expression of selenoproteins in E.coli.

Note: SECISDesign is not maintained anymore.

For articles describing the tool and webserver refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try SECISDesign with these examples:

Insert SECIS in MsrB (input|result)
Custom SECIS in MsrB (input|result)

Original Protein Sequence

Protein sequence (single letter amino acid codes or '#' for STOP)

SECIS Design Constraints

Position of Selenocystein in Protein:

Amino Acids to Conserve:

SECIS-Element:

FdhF-std	FdhF-std	FdhF-insert	FdhF-insert	FdhF-delete	FdhF-delete
	(optional)		(optional)		(optional)

$Custom structure: (optional) String length has to be in range (0,300). Maximally 1 line is allowed. Has to be of the alphabet '.,()[]{}GU/\' and its length has to be a multiple of 3 to encode codons. Click for further information!$

Custom structure:

Custom sequence:

[+] Similarity Scoring [-] Similarity Scoring

Similarity:

Insertion Penalty:

Deletion Penalty:

[+] RNAinverse (local search) [-] RNAinverse (local search)

Search Strategy:

Objective Function:

Valid Similarity Fraction:

Compared Similarity:

Probabilities of Bases:

Description:

Your Email:

(optional)
(optional)

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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