Repository translate_bed_sequences
Name: translate_bed_sequences
Owner: jjohnson
Synopsis: Perform 3 frame translation of BED file augmented with a sequence column
This tool takes an extended (12 column) BED input file that has been processed
by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
It generates a peptide fasta file with the 3-frame translations of the spliced sequence defined by each entry in the input BED file.
Typical workflow:  tophat splice_junctions.bed into Extract Genomic DNA into translate_bed_sequences
Link to this repository: https://toolshed.g2.bx.psu.edu/view/jjohnson/translate_bed_sequences/d328db400280
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/translate_bed_sequences
Type: unrestricted
Revision: 0:d328db400280
This revision can be installed: True
Times cloned / installed: 1021
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_numpy_1_7 revision 300877695495 owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
biopython 1.62 package

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
3 frame translation of BED augmented with a sequence column 0.0.1 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis