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Items tagged with "alignment" (31)

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Workflows (29)

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: 402 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)
Taverna 1 Original Uploader Steffen Möller	mustang provides structural alignment of two proteins (v3) Created: 20/08/08 @ 14:41:21 \| Last updated: 25/08/08 @ 15:40:45 Credits: Steffen Möller Attributions: Fetch PDB flatfile from RCSB server License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 140 times \| Downloaded: 59 times Tags (5): alignment \| bioinformatics \| grid \| pdb \| protein structure	View Download (v3)
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)
BioExtract Server Original Uploader Youguru...	SH2 domain screen in homo (v1) Created: 19/02/09 @ 16:34:22 \| Last updated: 08/06/09 @ 10:30:49 Credits: Youguruozhu License: Creative Commons Attribution-Share Alike 3.0 Unported License You can now Download this Workflow and import it into BioExtract Server at bioextract.org. This workflow retrieves a set of protein sequences containing SH2 domain in homo sapiens from NCBI GenBank Protein, then extracts the sequences of SH2 regions and performs a multiple alignment using EMMA and ClustalW. The alignment by EMMA is then plotted to PNG images, simultaneously creating a frequency matrix by prophecy. Finally scan a protein sequence queried with the frequency matrix using prophet. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 155 times \| Downloaded: 26 times Tags (1): alignment	View Download (v1)
Taverna 1 Original Uploader Jumblej...	fetch_fasta (v1) Created: 20/03/09 @ 11:22:45 \| Last updated: 20/03/09 @ 11:29:16 Credits: Jumblejumble License: Creative Commons Attribution-Share Alike 3.0 Unported License This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 155 times \| Downloaded: 71 times Tags (11): alignment \| beanshell \| blastall \| database \| FASTA \| fetch \| file \| list \| strings \| text \| tree	View Download (v1)
BioExtract Server Original Uploader Carol Lushbough	Multiple Protein Alignment Profiling(1) (v4) Created: 13/01/10 @ 18:52:45 \| Last updated: 17/11/10 @ 14:13:20 Credits: Carol Lushbough Alan Williams Attributions: A workflow version of the EMBOSS tutorial License: Creative Commons Attribution-Share Alike 3.0 Unported License Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 149 times \| Downloaded: 58 times Tags (7): alignment \| ebi \| emma \| genomics \| prettyplot \| profile \| tmap	View Download (v4)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and EMBOSS analysis (v1) Created: 03/07/09 @ 14:18:28 \| Last updated: 03/07/09 @ 14:19:32 Credits: Stian Soiland-Reyes Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 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: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 80 times \| Downloaded: 22 times Tags (6): alignment \| analysis \| sequence \| services \| soaplab \| workflow	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: 274 times \| Downloaded: 78 times Tags (5): alignment \| biomart \| clustalw \| emboss \| homology	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Kabsch Alignment of Small Molecules (v1) Created: 30/10/09 @ 22:12:57 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Aligns molecules using the Kabsch alignment and visualizes the results in the Jmol viewer. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 39 times Tags (5): alignment \| bioclipse \| cheminformatics \| chemistry \| kabsch	View Download (v1)
Taverna 1 Original Uploader Achille Zappa	M_Fetch_e-T_phylo_boot - (BETA) (v1) Created: 10/03/10 @ 15:44:02 \| Last updated: 10/03/10 @ 15:49:06 Credits: Achille Zappa Hamish McWilliam License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 11 times Tags (12): alignment \| analysis \| clustal \| consensus \| fetch \| ml \| muscle \| nj \| phylogeny \| protein \| sequence \| tree	View Download (v1)
Taverna 2 Original Uploader Bas Vroling	Create custom-made GPCR alignments (v1) Created: 24/08/10 @ 13:58:32 \| Last updated: 24/08/10 @ 13:58:35 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residue... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 21 times Tags (5): alignment \| ballesteros-weinstein \| gpcrdb \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_ParseBlast (v1) Created: 22/09/10 @ 12:40:55 \| Last updated: 22/09/10 @ 13:35:26 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 14 times Tags (9): alignment \| BLAST \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blat (v1) Created: 22/09/10 @ 13:18:55 \| Last updated: 22/09/10 @ 13:35:49 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 13 times Tags (9): alignment \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_Blat_ParseBlast (v1) Created: 22/09/10 @ 13:22:57 \| Last updated: 22/09/10 @ 13:36:12 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 15 times Tags (10): alignment \| BLAST \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
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	EMBL-EBI ClustalW2_SOAP (v1) Created: 17/01/11 @ 16:48:40 \| Last updated: 17/01/11 @ 16:48:37 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EMBL-EBI ClustalW2 (SOAP) EBI_ClustalW2 License: Creative Commons Attribution-Share Alike 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). This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Perform a ClustalW2 alignment using the EMBL-EBI’s C... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 12 times Tags (9): alignment \| async \| asynchronous services \| clustalw \| DNA \| ebi \| looping \| multiple sequence alignment \| protein	View Download (v1)
LONI Pipeline Original Uploader Pipeline	mrFAST Indexing and Mapping (v1) Created: 05/04/11 @ 21:47:48 \| Last updated: 05/04/11 @ 21:48:54 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License This page contains a number of bioinformatics workflows based on the mrFAST sequence analysis package. This page describes Pipeline bioinformatics modules from the mrFAST suite. mrFAST (micro-read Fast Alignment Search Tool) is mapper designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 6 bp. This manu... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 3 times Tags (4): alignment \| mapping \| mrfast \| pipeline	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)
BioExtract Server Original Uploader Carol Lushbough	tblastx non-redundant alignment (v1) Created: 30/06/11 @ 15:26:13 \| Last updated: 04/07/11 @ 16:51:41 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1. Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2. The output from ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 3 times Tags (7): alignment \| gene \| genomic \| proteins \| sequence \| species \| workflow	View Download (v1)
Mobyle Original Uploader Sebastien Carrere	Simple protein distance phylogeny workflow (v1) Created: 22/09/11 @ 16:47:46 \| Last updated: 22/09/11 @ 16:47:49 License: Creative Commons Attribution-Share Alike 3.0 Unported License Performs a multiple alignment and makes a phylogeny using a distance method on a set of protein sequences Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 5 times Tags (6): alignment \| distance \| phylogeny \| protein \| tree \| workflow	View Download (v1)

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Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:04:23 | Last updated: 07/08/09 @ 16:23:53

A tutorial to demonstrate how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

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Uploader:

Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

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