| Segmentation-fold is a application in the field of bioinformatics that predicts RNA 2D-structures. The model has an extension with respect to the classical Zuker algorithm, to allow new "structure elements" named segments and segmentloops. This makes it capable of folding a pre-defined substructure with multiple canonical or non-canonical base pairs, like K-turns and loop-E-motifs. Some of such sturcture elements are present in the corresponding energy table, although custom tables can be provided as well. We are currently optimizing the free energy parameters to improve accuracy. |
hg clone https://toolshed.g2.bx.psu.edu/repos/yhoogstrate/segmentation_fold
| Name | Version | Type | |
|---|---|---|---|
| htseq | 0.6.1 | package | |
| numpy | 1.9 | package | |
| pysam | 0.8.2.1 | package | |
| python | 2.7.10 | package | |
| segmentation-fold-utils | 2.1.0 | package | |
| segmentation-fold | 1.6.5 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place | smf-v1.6-5_utils-v2.1.0-2 | any | |
| Split entries over two files based on the estimated energy | smf-v1.6-5_utils-v2.1.0-1 | any | |
| RNA-Folding including predefined segments including K-turns | smf-v1.6-5_utils-v2.1.0-1 | any | |
| Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility | smf-v1.6-5_utils-v2.1.0-1 | any | |
| Finds all occurances of two given boxes (sequence motifs) within a FASTA file | smf-v1.6-5_utils-v2.1.0-1 | any | |
| Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file | smf-v1.6-5_utils-v2.1.0-3 | any | |
| Split entries into two files based on whether they overlap annotations in a bed file | smf-v1.6-5_utils-v2.1.0-1 | any | |
| Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file | smf-v1.6-5_utils-v2.1.0-1 | any | |