A workflow version of the EMBOSS tutorial
Created: 2011-01-27 04:14:45
Last updated: 2011-01-27 04:14:46
Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
Titles (1)
| A workflow version of the EMBOSS tutorial |
Descriptions (1)
| Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools. |
Dependencies (0)
Processors (15)
| Name |
Type |
Description |
| sequenceid |
stringconstant |
Valueswallid:ops2_* |
| msfFormat |
stringconstant |
Valuemsf |
| send |
stringconstant |
Value1171 |
| sbegin |
stringconstant |
Value110 |
| transeqSequenceID |
stringconstant |
Valueembl:xlrhodop |
| prophecyName |
stringconstant |
ValueOps2 Sequences |
| prophecyType |
stringconstant |
ValueG |
| seqret |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret |
| formatSequences |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret |
| emma |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma |
| prettyplot |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/display.prettyplot |
| tmap |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/protein_2d_structure.tmap |
| transeq |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq |
| prophecy |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophecy |
| prophet |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophet |
Outputs (3)
| Name |
Description |
| outputPlot |
|
| tmapPlot |
|
| prophetOutput |
|
Datalinks (17)
| Source |
Sink |
| sequenceid:value |
seqret:sequence_usa |
| seqret:outseq |
formatSequences:sequence_direct_data |
| msfFormat:value |
formatSequences:osformat |
| seqret:outseq |
emma:sequence_direct_data |
| emma:outseq |
prettyplot:sequences_direct_data |
| formatSequences:outseq |
tmap:sequences_direct_data |
| send:value |
transeq:send |
| sbegin:value |
transeq:sbegin |
| transeqSequenceID:value |
transeq:sequence_usa |
| prophecyName:value |
prophecy:name |
| prophecyType:value |
prophecy:type |
| emma:outseq |
prophecy:sequence_direct_data |
| prophecy:outfile |
prophet:infile_direct_data |
| transeq:outseq |
prophet:sequence_direct_data |
| prettyplot:Graphics_in_PNG |
outputPlot |
| tmap:Graphics_in_PNG |
tmapPlot |
| prophet:outfile |
prophetOutput |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
Credits (1)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Download Workflow
]
Reviews
(0)
No comments yet
Log in to make a comment