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Re-sequenced Daxx gene info

Created: 2009-04-08 17:53:46 | Last updated: 2009-08-10 12:30:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

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Next Generation Sequencing

Unique name: NextGenSeq
Created: Monday 23 November 2009 11:20:47 (UTC)

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Selenzyme

Created: 2017-08-18 08:23:47 | Last updated: 2017-08-23 11:12:00

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Genome annotation pipeline demonstrator wo... (2)

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Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320

Created: 2007-10-03

BLAST using DDBJ service (2)

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Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP...

Created: 2007-10-03 | Last updated: 2009-12-03

BLASTP with simplified results returned (2)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV...

Created: 2007-10-03 | Last updated: 2009-12-03

Simplify a BLAST text file (2)

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This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

Created: 2007-10-03 | Last updated: 2009-07-28

Multiple Blastp (2)

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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

Workflow for Protein Sequence Analysis (1)

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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.

Created: 2008-01-09 | Last updated: 2008-01-09

Credits: M.B.Monteiro

Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch

Retrieve sequence in EMBL format (3)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-06-17

Credits: Franck Tanoh Tomoinn Stuart Owen

BLASTP with simplified results returned (2)

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This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences.

Created: 2007-10-03 | Last updated: 2008-03-06

Retrieve Protein Sequence (1)

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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

Workflow Pattern - Sequence (1)

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This workflow is a GWorkflowDL representation of a sequence that sequentially invokes A and B. This workflow is equivalent to the following pseudo code: end_A = A(); end_B = B(end_A);

Created: 2008-12-03

Credits: Andreas Hoheisel

Biomart Protein Sequence Retrieval (1)

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

Created: 2009-03-09

Credits: Kieren Lythgow

DOI Record Generator (1)

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This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file.

Created: 2009-04-29

Credits: Andrea Wiggins

Attributions: Data Set Metadata Generator

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: Stian Soiland-Reyes

Attributions: Using CQL to query protein sequence data

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: cory (Kazuki Oshita)

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: cory (Kazuki Oshita)

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: cory (Kazuki Oshita)

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: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (3)

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This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2011-01-09

Credits: cory (Kazuki Oshita)

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: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

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: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

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

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: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

DNA sequence analysis pilot (1)

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  http://amc-app1.amc.sara.nl/twiki/bin/view/         Workflow-based  DNA sequence analysis on the Dutch Life Science Grid, presented as Application Showcase at the NBIC Conference 2009, Lunteren, The Netherlands, 17 & 18 March 2009. http://www.biomedgrid.it/programme may 15th 2009. Hands on workflow: grid-enabled medical imaging  (Johan Montagnat – Tristan Glatard)  

Created: 2009-07-10 | Last updated: 2009-11-30

Credits: Angela Luijf Glatard

DNA sequence analysis pilot (Blat) (2)

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http://amc-app1.amc.sara.nl/twiki/bin/view/  Workflow-based  DNA sequence analysis on the Dutch Life Science Grid. This workflow is  based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis    

Created: 2009-11-20 | Last updated: 2009-11-30

Credits: Angela Luijf Barbera van Schaik Glatard

Attributions: DNA sequence analysis pilot

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: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

Retrieve Genome Seqn using gi nos (1)

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

Created: 2010-03-19

Credits: Ian Laycock nclteamc

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

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Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta...

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

Credits: cory (Kazuki Oshita)

retrieve protein sequence and do a high sp... (1)

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retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

retrieve protein sequence and do a BLAST w... (1)

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retrieve protein sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html exxample accession : Q9NRA8 database : UNIPROT program : blastp param : -b 5 -m 7    

Created: 2010-07-21 | Last updated: 2010-09-01

Credits: Lebreton

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn    

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

Attributions: BLAST using DDBJ service

retrieve nucleotide sequence and do a high... (4)

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retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

Created: 2010-07-21 | Last updated: 2010-09-07

Credits: Lebreton

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

retrieve nucleotide sequence and do a VecS... (1)

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retrieve nucleotide sequence and do a VecScreen from DDBJ Web services : A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin   informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100

Created: 2010-07-21 | Last updated: 2010-09-01

Credits: Lebreton

BLAST against the GPCRDB (1)

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With this workflow you can submit a BLAST query to the GPCRDB. Input requires a sequence with amino acids only.

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

Create custom-made GPCR alignments (1)

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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...

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

M_Fetch_e-T_phylo_boot - (BETA) (1)

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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.

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Achille Zappa Hamish McWilliam

retrieve protein sequence and do a high sp... (1)

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retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services

retrieve protein sequence and do a BLAST f... (1)

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retrieve protein sequence and do a BLAST from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve protein sequence and do a BLAST and extract position from DDBJ Web services

retrieve nucleotide sequence and do a high... (1)

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retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn 

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services

Sff2Fasta_Blast_ParseBlast (1)

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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/      

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Sff2Fasta_Blat (1)

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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/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Sff2Fasta_Blast_Blat_ParseBlast (1)

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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/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

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: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: Katy Wolstencroft

BiomartAndEMBOSSDisease (4)

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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

DAS sequence retrieval (2)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS sequence retrieval and parsing with JDAS (1)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS features retrieval (2)

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Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).

Created: 2011-06-01 | Last updated: 2011-06-01

Credits: Rafael C. Jimenez

tblastx non-redundant alignment (1)

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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 ...

Created: 2011-06-30 | Last updated: 2011-07-04

Credits: Carol Lushbough

EBI NCBI BLAST Multi FASTA (2)

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This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It 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. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm...

Created: 2011-07-16 | Last updated: 2011-07-16

Credits: Rafael C. Jimenez

BLAST your sequences against the NucleaRDB (1)

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BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc)

Created: 2011-08-19 | Last updated: 2011-08-19

Credits: Bas Vroling

KEIO Bioinformatics Web Service - a genera... (2)

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This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl...

Created: 2010-08-13 | Last updated: 2010-11-19

Credits: cory (Kazuki Oshita)

(Updated)Retrieve sequence in EMBL format. (1)

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This workflow retrieves a sequence associated with its features in embl format.

Created: 2012-03-19 | Last updated: 2012-04-02

Credits: Ankit upadhyay

NCBI Protein Clustal Omega Alignment (1)

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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: Carol Lushbough

Non-redundant protein alignments (1)

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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: Carol Lushbough

Blast_Align_and_Tree (2)

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This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are ...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: Protein_search_fetch_align_tree

Blast_and_Interproscan (5)

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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. The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequenc...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

InterproScan_Example (3)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished.

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

clustal_phylogeny (3)

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This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip.

Created: 2013-01-28 | Last updated: 2013-03-11

Credits: Katy Wolstencroft

Antibiotic resistance profiling (1)

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 A workflow that takes a user defined genomic sequence and queries a third party database of genes encoding antibiotic resistance through a BLAST search for matching sequences. The accession IDs from the matches are extracted and the Entrez webservice is used to retrieve genbank records for the antibiotic resistance genes found. A python script is essential in the functioning of this workflow and this can be found at www.bioinformatix.co.uk along with a user and maintenance manual whic...

Created: 2013-03-08

Credits: Team A

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

Analyze any DNA sequence, EMBL (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in EMBL format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual wo...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, Fasta (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in Fasta format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual w...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, GeneBank (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in GeneBank format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individua...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence for site enrichment (1)

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This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Detrprok (4)

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In the case study of stranded and prokaryotic RNAseq data, the Det'Rprok workflow detects candidates of 3 kinds of non coding RNA: 5'UTRs, antisense RNAs, and small RNAs.Inputs: i) an mapping file (bam format) containing one valid alignment by read, ii) a feature file (gff format) annotating the genomic sequences used for the mapping. Dependencies (from the Galaxy toolshed): "s_mart", "detrprok_scripts"

Created: 2013-05-20 | Last updated: 2015-11-03

Workflow for Selenzyme v 1.0 (2)

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Created: 2017-08-18 | Last updated: 2017-09-08

Credits: Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell