All content

BiomartAndEMBOSSDisease (4)

• Download

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

EMBL-EBI ClustalW2 (SOAP) (1)

• Download

Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: EBI_ClustalW2

A Basic example R workflow (3)

• Download

This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: Alan Williams

genePattern data preprocessing (2)

• Download

preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default preprocess data set using genePattern preProces service, the input should be in genePattern STATML format.preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: Wei Tan

Keyword search against chEMBL (1)

• Download

Created: 2010-03-24

Credits: Annsofie Anderssson

KEGG pathway analysis (1)

• Download

The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi...

Created: 2010-03-19

Credits: Baywatch Solutions

Kegg pathway diagrams (missing part 3) (2)

• Download

Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of...

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

Credits: Gregg Iceton

Retrieve Genome Seqn using gi nos (1)

• Download

Retrieves the genome seqn for both the target and source strains using gi nos

Created: 2010-03-19

Credits: Ian Laycock nclteamc

Extract proteins from xml blast results (1)

• Download

The workflow extracts a list of proteins from the target genome that may be known drugs using the blast similarity results.

Created: 2010-03-19

Credits: Ian Laycock nclteamc

Parse unique proteins from Blast file (1)

• Download

The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.

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

Credits: Ian Laycock nclteamc