Input and runtime details for job 7036761 (precomputed example)

Constraints

	Structure constraint		AAAAAAAAAACCCCCCC(((((....(((((....(((.....))).)))))....)))))CCCCCCCBBBBBBBBBB
	Sequence constraint		not provided
	Targeted GC-content [0..1]		0.6
	Maximum for uniform distribution sampling		not provided
	Variance for normal distribution sampling		not provided

Constraint

	Allow GU base pairs		yes
	Allow pseudoknots		no

Energy

Folding temperature

37.0

AntaRNA

	Max. terrain resets		5
	Convergence counts		130
	Ant termination criterion		50
	Probability weight alpha		1.0
	Probability weight beta		1.0
	Pheromone evaporation rate		0.2
	Constraint weight structure		0.5
	Constraint weight sequence		1.0
	Constraint weight GC-value		5.0
	Random seed		not provided

Output

Number of sequences

Job ID 7036761 (server version 4.0.0)

	Job Submitted & Queued		@ Fri Jun 19 13:31:08 CEST 2015
	AntaRNA Started		@ Fri Jun 19 13:31:22 CEST 2015
	AntaRNA Finished & Post-Processing		@ Fri Jun 19 13:41:57 CEST 2015
	Post-Processing Finished		@ Fri Jun 19 13:41:58 CEST 2015
	Job Completed		@ Fri Jun 19 13:41:58 CEST 2015

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7036761&toolName=AntaRNA ( 30 days expiry )

Description of the job

Design a SECIS element with flexible stem length (block C) and flanking context (blocks A and B). See Help page for further information.

Design a SECIS element with flexible stem length (block C) and flanking context (blocks A and B). Note, where upper case symbols are used the according block has to show at least one base pair in the final design. The design is visualized in the following figure.

SECIS design with block constraints

Output download complete results [zip]

Designed sequences

Name	Sequence & mfe	GC%	dStr%	dSeq%	dGC%
Target	AAAAAAAAAACCCCCCC(((((....(((((....(((.....))).)))))....)))))CCCCCCCBBBBBBBBBB	60.0
antaRNA_0	ACCCCUAUAGCCGAGCCCACCCAAAAACGGAACCCCGCGUGUAGCGAUCCGUCCUCGGGUGAUGGAACCUGAAAGCCU ...............(((((((....(((((....(((.....))).)))))....)))))..)).............	60.2	2.5	0.0	0.0
antaRNA_1	CGACACUCACAUAGGACGGCACUUGCCGACGCAUUGGCGUUCUGCCCCGUCGAACUGUGCCACAACCACCCCAAACUC .............((..(((((....(((((....(((.....))).)))))....)))))....))...........	60.2	2.5	0.0	0.0
antaRNA_2	CCCCUCUGGGUCUAGAACCCCCUAAAUGCCAACGAGACGUGCAGUCAUGGCACUCUGGGGGCUCCGUUCAAGCUCGUG (((....)))....((.(((((....(((((....(((.....))).)))))....))))).))..............	60.2	1.2	0.0	0.0
antaRNA_3	AGGAAAUCCAACACAGCGCGCUAUACCCGAAAACGCCCGAACUGGGAUUCGGCCCAGGCGCACCCCACACAGCUAAAC .((....))......(.(((((....(((((....(((.....))).)))))....))))).)...............	58.9	1.2	0.0	0.0
antaRNA_4	CGCACCCCAAUCCCAGAGCGCCGUCACCUCCCCUGACAAGAACUGUAGGAGGCACAGGCGCUGAACAACUCAUUGAGA ................((((((....(((((....(((.....))).)))))....))))))......(((...))).	58.9	1.2	0.0	0.0
antaRNA_5	CCGACGGGCUUACGGCAGCCCAUACUGCGCUGGUAAUCGAAAUGAUAGGCGUACGCUGGGCGCCCACUUUGACUUCAC ((....)).....(((.(((((...((((((....(((.....))).))))))...))))))))..............	58.9	2.5	0.0	0.0
antaRNA_6	CCGGAACCGGCAAUCCUCGCUUAAUACGCUCGAUCCAGGCCGACUGAGGGCGCAAGAAGUGCUGACACCACUCUAAGG (((....)))...((..(((((....(((((....(((.....))).)))))....)))))..)).............	58.9	1.2	0.0	0.0
antaRNA_7	UGCCCCAUUCCAGAUUAGACCACCAUACGCUACAUGCCCCCGAGGCCGGCGUUCCCUGGUUCCCCUGACGUUUUACGA ..........(((....(((((....(((((....(((.....))).)))))....)))))...))).(((...))).	58.9	1.2	0.0	0.0
antaRNA_8	ACCAUACCACCAACCGACGGCUUACGGCACCUGUAGGCGAAAAGCCCGGUGUGAACGGCCGAGGUACAUACCGAUCCG ............(((..(((((....(((((....(((.....))).)))))....))))).))).............	60.2	2.5	0.0	0.0
antaRNA_9	AUCCUCACAGCCUUUGUGGGCUCAUGCCGCCCCGAGCCCUCAAGGUAGGCGGAGAUAGCCCAUCACAGUUCCAAACGU ...............(((((((....(((((....(((.....))).)))))....)))))))...............	58.9	2.5	0.0	0.0

Download:

Visualization of the selected sequence

[save as SVG] Explicit constraint violations are highlighted in red. Visualization done with forna (Kerpedjiev et al., 2015)

Job resubmission

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

usability assessment

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When using AntaRNA please cite :

Robert Kleinkauf, Martin Mann and Rolf Backofen
AntaRNA - Ant Colony Based RNA Sequence Design
Bioinformatics, 31(19), pages 3114-3121, 2015.
Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, and Martin Mann
AntaRNA - multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
BMC Bioinformatics, 16(1), pages 1-7, 2015.
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 AntaRNA version 1.1.2 using Vienna RNA package 2.1.8 or pKiss (2014-03-17)

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