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Items tagged with "sequence alignment" (13)

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Workflows (13)

Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW2 (v2) Created: 07/04/09 @ 20:06:03 \| Last updated: 06/12/10 @ 11:00:19 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 479 times \| Downloaded: 229 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW_alignment_tree (v2) Created: 31/05/08 @ 13:53:04 \| Last updated: 03/12/10 @ 13:34:43 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree License: Creative Commons Attribution 3.0 Unported License Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 167 times \| Downloaded: 79 times Tags (10): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| sequence alignment \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 403 times \| Downloaded: 133 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
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: 185 times \| Downloaded: 52 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	EBI_Kalign (v1) Created: 02/06/08 @ 21:28:56 \| Last updated: 06/12/10 @ 11:39:52 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 70 times \| Downloaded: 43 times Tags (6): alignment \| bioinformatics \| ebi \| kalign \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MAFFT (v1) Created: 03/06/08 @ 05:55:43 \| Last updated: 06/12/10 @ 11:38:58 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 91 times \| Downloaded: 53 times Tags (6): alignment \| bioinformatics \| ebi \| mafft \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MUSCLE (v1) Created: 03/06/08 @ 06:16:22 \| Last updated: 06/12/10 @ 11:04:03 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used. Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 106 times \| Downloaded: 55 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| muscle \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_TCoffee (v1) Created: 03/06/08 @ 06:31:37 \| Last updated: 06/12/10 @ 11:02:53 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used. Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 122 times \| Downloaded: 59 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| sequence alignment \| t-coffee	View Download (v1)
BioExtract Server Original Uploader Carol Lushbough	Liliopsida Protein Alignment (v6) Created: 13/01/10 @ 18:42:35 \| Last updated: 17/11/10 @ 13:46:04 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW. Rating: 4.0 / 5 (1 rating) \| Versions: 6 \| Reviews: 0 \| Comments: 3 \| Citations: 1 Viewed: 536 times \| Downloaded: 105 times Tags (5): alignment \| bioextract \| multiple sequence alignment \| nucleotide \| sequence alignment	View Download (v6)
Taverna 2 Original Uploader Hamish McWilliam	EMBL-EBI ClustalW2 (SOAP) (v1) Created: 06/12/10 @ 13:16:52 Attributions: EBI_ClustalW2 License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 16 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	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: 8 times \| Downloaded: 7 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: 12 times \| Downloaded: 8 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: 97 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)