All content

BiomartAndEMBOSSAnalysis (4)

• Download

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: 2009-09-15 | Last updated: 2015-01-26

Multiple Blastp (2)

• Download

This is a workflow to automate multiple BLASTp jobs on a large list of protein sequences in FASTA format.

Created: 2007-11-20 | Last updated: 2008-01-10

Credits: Kieren Lythgow

mustang provides structural alignment of t... (3)

• Download

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.

Created: 2008-08-20 | Last updated: 2008-08-25

Credits: Steffen Möller

Attributions: Fetch PDB flatfile from RCSB server

Retrieve Protein Sequence (1)

• Download

Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

Created: 2008-07-30 | Last updated: 2009-12-03

Credits: Katy Wolstencroft

MassBank to KEGG (1)

Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Retrieve Single Molecule from ZINC - struc... (1)

• Download

The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst...

Created: 2008-08-24 | Last updated: 2008-08-25

Credits: Steffen Möller

getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

• Download

uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image

Created: 2008-06-05 | Last updated: 2008-06-16

Credits: Michael Gerlich

Search InChI in NCBI eSearch (pccompound) (1)

• Download

This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Download Entries from PubChem (1)

• Download

Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results. Adding support for downloading this XML file and writing it to filesystem is planned.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

runFunCUT (1)

MOBY Web Services (synchronous and asynchronous) that describe the FunCUT method. Is recommended use asynchronous MOBY services because the method needs huge range of time.   FunCUT Method Short Description: Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups) FunCUT (Abascal and Valencia, 2003. PROTEINS: Structure, Function, and Genetics 53:683– 692 (2003)) is application based on the study...

Created: 2008-10-03 | Last updated: 2008-10-03

Credits: José Manuel Rodríguez