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Original Uploader

Alan Williams

A workflow version of the EMBOSS tutorial (v1)

Created: 05/03/08 @ 14:05:20 | Last updated: 25/03/08 @ 14:43:35

Credits: Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 303 times | Downloaded: 104 times

Original Uploader

Hamish McWilliam

Sequence_or_ID (v1)

Created: 01/06/08 @ 14:15:12

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 111 times | Downloaded: 42 times

Original Uploader

Hamish McWilliam

Protein_transmembrane_prediction (v2)

Created: 26/10/08 @ 21:16:10

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

License: Creative Commons Attribution 3.0 Unported License

Transmembrane and signal peptide prediction using three methods: EMBOSS tmap with a single sequence. Uses Soaplab tmap. Phobius. Uses EBI's WSPhobius web service. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 206 times | Downloaded: 55 times

Original Uploader

Katy Wolstencroft

BioMart and Emboss Analysis (T2) (v1)

Created: 15/09/09 @ 15:05:11

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 176 times | Downloaded: 35 times