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Items tagged with "emboss" (7)

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Workflows (7)

Taverna 1

Original Uploader

Alan Williams

BiomartAndEMBOSSAnalysis (v3)

Created: 05/03/08 @ 14:01:18 | Last updated: 01/09/08 @ 13:57:23

License: Creative Commons Attribution 3.0 License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 701 times | Downloaded: 617 times

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Taverna 1

Original Uploader

Alan Williams

A workflow version of the EMBOSS tutorial (v1)

Created: 05/03/08 @ 14:05:21 | Last updated: 25/03/08 @ 14:43:36

Credits: Tomoinn

License: Creative Commons Attribution 3.0 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: 481 times | Downloaded: 417 times

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:30 | Last updated: 01/06/08 @ 12:20:31

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 License

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3. Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webs...

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

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Taverna 1

Original Uploader

Hamish McWilliam

Sequence_or_ID (v1)

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

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 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: 282 times | Downloaded: 225 times

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Taverna 1

Original Uploader

Hamish McWilliam

tmap_single_sequence (v2)

Created: 01/06/08 @ 14:27:13 | Last updated: 02/06/08 @ 21:38:13

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

License: Creative Commons Attribution 3.0 License

Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 288 times | Downloaded: 274 times

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_transmembrane_prediction (v2)

Created: 01/06/08 @ 17:49:32 | Last updated: 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 License

Transmembrane and signal peptide prediction using three methods: 1. EMBOSS tmap with a single sequence. Uses Soaplab tmap. 2. Phobius. Uses EBI's WSPhobius web service. 3. 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: 348 times | Downloaded: 314 times

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Taverna 1

Original Uploader

Hamish McWilliam

Nucleotide_ORF_translation (v1)

Created: 06/06/08 @ 20:13:05

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

License: Creative Commons Attribution 3.0 License

From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).

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

Viewed: 236 times | Downloaded: 195 times

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