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Items tagged with "emboss" (13)

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Workflows (13)

Taverna 1 Original Uploader Alan Williams	BiomartAndEMBOSSAnalysis (v4) Created: 15/09/09 @ 15:11:11 License: Creative Commons Attribution 3.0 Unported 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: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1157 times \| Downloaded: 391 times Tags (6): bioinformatics \| biomart \| emboss \| example \| mygrid \| taverna	View Download (v4)
Taverna 1 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: 393 times \| Downloaded: 136 times Tags (4): emboss \| example \| mygrid \| taverna	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Protein_alignment_transmembrane (v1) Created: 01/06/08 @ 12:20:29 Credits: Hamish McWilliam Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch License: Creative Commons Attribution 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 190 times \| Downloaded: 57 times Tags (16): alignment \| bioinformatics \| clustal \| clustalw \| dbfetch \| ebi \| emboss \| emboss tmap \| FASTA \| multiple sequence alignment \| protein \| protein annotation \| sequence alignment \| sequence similarity search \| transmembrane \| transmembrane prediction	View Download (v1)
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 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: 144 times \| Downloaded: 60 times Tags (6): bioinformatics \| dbfetch \| ebi \| emboss \| emboss seqret \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	tmap_single_sequence (v2) Created: 01/06/08 @ 14:27:12 \| Last updated: 02/06/08 @ 21:38:13 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported 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: 116 times \| Downloaded: 44 times Tags (9): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_transmembrane_prediction (v2) Created: 26/10/08 @ 21:16:10 \| Last updated: 01/04/11 @ 08:57:10 Credits: Hamish McWilliam Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence License: Creative Commons Attribution 3.0 Unported License 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... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 3 \| Citations: 0 Viewed: 320 times \| Downloaded: 91 times Tags (11): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| interproscan \| phobius \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Nucleotide_ORF_translation (v1) Created: 06/06/08 @ 20:13:04 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported 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: 185 times \| Downloaded: 96 times Tags (8): bioinformatics \| ebi \| emboss \| emboss getorf \| nucleotide sequence \| nucleotide translation \| open reading frame \| ORF	View Download (v1)
Taverna 2 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: 292 times \| Downloaded: 85 times Tags (5): alignment \| biomart \| clustalw \| emboss \| homology	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast (v1) Created: 13/12/10 @ 14:41:12 \| Last updated: 13/12/10 @ 15:15:45 Attributions: BLAST using DDBJ service License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 9 times Tags (15): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast with concatinated gene id (v1) Created: 13/12/10 @ 14:41:39 \| Last updated: 13/12/10 @ 14:47:55 Attributions: BLAST using DDBJ service Biomart and Blast License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 11 times Tags (9): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BiomartAndEMBOSSAnalysis (v4) Created: 27/01/11 @ 17:03:03 \| Last updated: 12/05/11 @ 13:31:41 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 102 times \| Downloaded: 55 times Tags (16): alignment \| biomart \| biomart emboss \| bonn \| disease \| emboss \| emma \| ensembl \| gene \| genes \| homolog \| human \| mouse \| sequence \| sequence alignment \| soaplab	View Download (v4)
LONI Pipeline Original Uploader Pipeline	EMBOSS-Matcher Pipeline Workflow (v1) Created: 05/04/11 @ 21:34:49 \| Last updated: 14/07/11 @ 01:52:02 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 5 times Tags (3): emboss \| matcher \| pipeline	View Download (v1)
Taverna 2 Original Uploader Alan Williams	BiomartAndEMBOSSDisease (v2) Created: 12/07/11 @ 12:54:05 \| Last updated: 19/03/12 @ 15:31:14 Credits: Katy Wolstencroft Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 12 times Tags (4): biomart \| emboss \| example \| taverna	View Download (v2)