A workflow version of the EMBOSS tutorial
Created: 2009-07-03 14:50:54
Last updated: 2009-07-03 14:51:15
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.
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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_* |
| prophecyName |
stringconstant |
ValueOps2 Sequences |
| prophecyType |
stringconstant |
ValueG |
| send |
stringconstant |
Value1171 |
| sbegin |
stringconstant |
Value110 |
| transeqSequenceID |
stringconstant |
Valueembl:xlrhodop |
| msfFormat |
stringconstant |
Valuemsf |
| tmap |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/protein_2d_structure.tmap |
| formatSequences |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret |
| prophet |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophet |
| seqret1 |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret |
| prophecy |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophecy |
| transeq |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq |
| plot |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot |
| emma |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma |
Outputs (3)
| Name |
Description |
| outputPlot |
|
| prophetOutput |
|
| tmapPlot |
|
Datalinks (17)
| Source |
Sink |
| formatSequences:outseq |
tmap:sequences_direct_data |
| seqret1:outseq |
formatSequences:sequence_direct_data |
| msfFormat:value |
formatSequences:osformat |
| transeq:outseq |
prophet:sequence_direct_data |
| prophecy:outfile |
prophet:infile_direct_data |
| sequenceid:value |
seqret1:sequence_usa |
| prophecyType:value |
prophecy:type |
| emma:outseq |
prophecy:sequence_direct_data |
| prophecyName:value |
prophecy:name |
| send:value |
transeq:send |
| transeqSequenceID:value |
transeq:sequence_usa |
| sbegin:value |
transeq:sbegin |
| emma:outseq |
plot:sequences_direct_data |
| seqret1:outseq |
emma:sequence_direct_data |
| plot:Graphics_in_PNG |
outputPlot |
| prophet:outfile |
prophetOutput |
| tmap:Graphics_in_PNG |
tmapPlot |
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