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BiomartAndEMBOSSAnalysis (4)

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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.

Created: 2009-09-15 | Last updated: 2015-01-26

A workflow version of the EMBOSS tutorial (1)

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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.

Created: 2008-03-05 | Last updated: 2008-03-25

Credits: Tomoinn

Protein_alignment_transmembrane (1)

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

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

Sequence_or_ID (1)

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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.

Created: 2008-06-01

Credits: Hamish McWilliam

tmap_single_sequence (2)

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

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

Protein_transmembrane_prediction (2)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Transmembrane and signal...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

Nucleotide_ORF_translation (1)

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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).

Created: 2008-06-06

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

BioMart and Emboss Analysis (T2) (1)

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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...

Created: 2009-09-15

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

Biomart and Blast (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service

Biomart and Blast with concatinated gene id (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service Biomart and Blast

BiomartAndEMBOSSDisease (4)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. 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.

Created: 2011-01-27 | Last updated: 2012-09-04

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

EMBOSS-Matcher Pipeline Workflow (1)

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This page contains a number of bioinformatics workflows based on the advanced EMBOSS informatics package. This page describes as Pipeline modules several bioinformatics tools from the EMBOSS suite and demonstrates the construction of a couple of integrated pipeline workflows (end-to-end bioinformatics solutions via the LONI Pipeline). Matcher finds the best local alignments between two sequences. It can be used to compare two sequences looking for local sequence similarities using a ri...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

BiomartAndEMBOSSDisease (2)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: Katy Wolstencroft

Attributions: BiomartAndEMBOSSDisease