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Repository graphclust_fasta_to_gspan
Name: graphclust_fasta_to_gspan
Owner: rnateam
Synopsis: Second step of GraphClust
For each fragment of input sequence RNAshapes is used to create a set of structures. The default parameters for example consider for each input fragment again a window of size 40nt and 150nt with a window shift of 30%. This allows to consider local structures as well as global structures for a fragment. From each such RNAshape window we take the top 5 shreps (suboptimal structures for the top 5 shapes) within 20% of the mfe energy of that window and convert them into graphs. As shape level (abstraction level) we use 3 for short sequences and 5 for sequences >= 80nt. Please see also RNAshapes documentation for all these terms.
Development repository: https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN
Link to this repository: https://toolshed.g2.bx.psu.edu/view/rnateam/graphclust_fasta_to_gspan/d2784e70dd19
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_fasta_to_gspan
Type: unrestricted
Revision: 9:d2784e70dd19
This revision can be installed: True
Times cloned / installed: 1252

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Name Description Version Minimum Galaxy Version
0.4 16.01

Categories
RNA - Utilities for RNA