Input and runtime details for job 4894743 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 4894743 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:26 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:36:09 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 05:38:38 CET 2018
	Post-Processing Finished		@ Sat Feb 17 05:38:45 CET 2018
	Job Completed		@ Sat Feb 17 05:39:16 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

Output

Download an archive file containing the complete results produced by the job in [.zip] format.

Results file content

Warning: your run directory contains many files (23). In general it is suggested to run CopraRNA in an empty directory to avoid unexpected behaviour. # INFO : Sequence 'I33_RS19220' contains ambiguous IUPAC nucleotide encodings. These positions are ignored for interaction computation and replaced by 'N'.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
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 CopraRNA version 2.1.2

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