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Showing 29 results. Use the filters on the left and the search box below to refine the results.
Type: Taverna 2 Tag: sequence Licence: by-sa

Workflow EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: User Stian Soiland-Reyes User Katy Wolstencroft User Paolo User Hamish McWilliam

Attributions: Workflow EBI_InterProScan for Taverna 2 Workflow EBI InterproScan T2 Workflow EBI_InterProScan Workflow EBI InterProScan

Workflow EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-01-26 | Last updated: 2010-01-26

Credits: User Stian Soiland-Reyes User Paolo User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

Workflow Compare genome, extract proteins which are... (1)

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  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

Attributions: Workflow fetchEnsemblSeqsAndBlast Workflow NCBI Gi to Kegg Pathways Workflow color_pathway_by_objects

Workflow Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

Workflow Biomart and EMBOSS analysis (1)

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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: 2009-07-03 | Last updated: 2009-07-03

Credits: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

Workflow G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: User cory (Kazuki Oshita)

Workflow G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: User cory (Kazuki Oshita)

Workflow G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: User cory (Kazuki Oshita)

Workflow G-language Genome Analysis Environment - B... (2)

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This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: User cory (Kazuki Oshita)

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