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Tag: bioinformatics Licence: by-sa

Workflow 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: User José Manuel Rodríguez

Workflow Retrieve Pathways and Compound information... (1)

Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

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

Credits: User Michael Gerlich

Workflow dbfetch tutorial (1)

This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is alw...

Created: 2008-09-22

Credits: User Steffen Möller

Workflow Sequences Alignment and Sorting by Coordinate (1)

We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz Alignment via Burrows-Wheeler transformation using BWA-MEM algorithm Sorts the input SAM or BAM Post Alignment File Processing We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz MarkDuplicates examines aligned records in the supplied SAM or BAM f...

Created: 2016-05-16 | Last updated: 2016-07-06

Workflow Variant Annotation with VEP (Variant Effec... (1)

Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2016-05-16 | Last updated: 2016-07-06

Workflow DatabaseID to ConceptID (7)

Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics


Workflow Scoring small molecules for metabolite lik... (2)

 Prerequisite:   - CDK -Taverna Plugin 0.5.1 - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

Workflow Non-redundant protein alignments (1)

Execute BLASTP program to search protein databases using a protein query: Input file from iPlant Discovery Environment Save the data extract of similar sequences created by BLASTP Execute XMKNR to a compute a non-redundant set from a large collection of protein sequences. Input from the data extract created by BLASTP. Perform multiple sequence alignments using Clustal Omega and TCoffee Input from data extract created by XMKNR To execute this workflow, you need to be logged into the Bio...

Created: 2012-12-19 | Last updated: 2012-12-19

Credits: User Carol Lushbough

Workflow NCBI Protein Clustal Omega Alignment (1)

Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

Created: 2012-08-31

Credits: User Carol Lushbough

Workflow Match gene lists based on information in l... (7)

[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

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