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Items tagged with "sequence" (56)

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Network-member Next Generation Sequencing

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

This group is for people wishing to contribute / find out more about 'Next Generation Sequencing' technology and data. Please feel free to join this group and add any workflows you think others may benefit from.

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Blob Re-sequenced Daxx gene info

Created: 08/04/09 @ 17:53:46 | Last updated: 10/08/09 @ 12:30:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344

File type: Excel workbook

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 30 times | Downloaded: 22 times

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Workflows (54)
Original Uploader

Workflow Genome annotation pipeline demonstrator wo... (2)

Created: 03/10/07 @ 18:35:47

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 592 times | Downloaded: 178 times

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Workflow BLAST using DDBJ service (2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:31:20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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...

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 640 times | Downloaded: 234 times

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Workflow BLASTP with simplified results returned (2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:28:50

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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...

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 344 times | Downloaded: 115 times

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Workflow Simplify a BLAST text file (2)

Created: 03/10/07 @ 18:36:06 | Last updated: 28/07/09 @ 13:01:45

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 392 times | Downloaded: 151 times

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Original Uploader

Workflow Multiple Blastp (2)

Created: 20/11/07 @ 16:58:38 | Last updated: 10/01/08 @ 12:09:38

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 517 times | Downloaded: 165 times

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Workflow Workflow for Protein Sequence Analysis (1)

Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1795 times | Downloaded: 467 times

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Original Uploader

Workflow Retrieve sequence in EMBL format (3)

Created: 17/06/09 @ 16:51:32

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 330 times | Downloaded: 108 times

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Original Uploader

Workflow BLASTP with simplified results returned (2)

Created: 03/10/07 @ 18:36:12 | Last updated: 06/03/08 @ 17:01:32

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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.

Rating: 4.0 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 240 times | Downloaded: 64 times

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Original Uploader

Workflow Retrieve Protein Sequence (1)

Created: 30/07/08 @ 16:36:55 | Last updated: 03/12/09 @ 16:54:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 394 times | Downloaded: 131 times

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Original Uploader

Workflow Workflow Pattern - Sequence (1)

Created: 03/12/08 @ 14:17:20

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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);

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 59 times | Downloaded: 33 times

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Original Uploader

Workflow Biomart Protein Sequence Retrieval (1)

Created: 09/03/09 @ 11:38:10

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 200 times | Downloaded: 48 times

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Workflow DOI Record Generator (1)

Created: 29/04/09 @ 16:39:57

Credits: User Andrea Wiggins

Attributions: Workflow Data Set Metadata Generator

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 115 times | Downloaded: 35 times

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Workflow Using CQL to query protein sequence data (1)

Created: 07/05/09 @ 14:28:59

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 178 times | Downloaded: 76 times

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Original Uploader

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

Created: 05/04/10 @ 06:20:58

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 53 times | Downloaded: 23 times

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Original Uploader

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

Created: 05/04/10 @ 06:24:02

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 56 times | Downloaded: 37 times

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

Created: 05/04/10 @ 06:13:16 | Last updated: 05/04/10 @ 06:13:17

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 22 times

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Original Uploader

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

Created: 05/04/10 @ 06:22:28

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 68 times | Downloaded: 27 times

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Original Uploader

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

Created: 05/04/10 @ 06:17:25 | Last updated: 09/01/11 @ 06:08:19

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 25 times

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Original Uploader

Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:46:07 | Last updated: 26/01/10 @ 14:46:08

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

Attributions: Workflow EBI InterproScan T2 Workflow EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 198 times | Downloaded: 129 times

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Workflow EBI_InterProScan for Taverna 2 (2)

Created: 26/01/10 @ 14:45:46 | Last updated: 24/11/10 @ 10:04:09

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 456 times | Downloaded: 210 times

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Workflow Biomart and EMBOSS analysis (1)

Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:32

Credits: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 98 times | Downloaded: 25 times

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Original Uploader

Workflow DNA sequence analysis pilot (1)

Created: 10/07/09 @ 14:31:27 | Last updated: 30/11/09 @ 09:37:38

Credits: User Angela Luijf User Glatard

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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)  

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 354 times | Downloaded: 49 times

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Workflow DNA sequence analysis pilot (Blat) (2)

Created: 20/11/09 @ 11:12:43 | Last updated: 30/11/09 @ 09:35:38

Credits: User Angela Luijf User Barbera van Schaik User Glatard

Attributions: Workflow DNA sequence analysis pilot

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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    

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 99 times | Downloaded: 23 times

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

Created: 19/03/10 @ 13:16:24 | Last updated: 19/03/10 @ 13:33:53

Credits: User Ian Laycock Network-member nclteamc

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 176 times | Downloaded: 67 times

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Workflow Retrieve Genome Seqn using gi nos (1)

Created: 19/03/10 @ 15:17:53

Credits: User Ian Laycock Network-member nclteamc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 12 times

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

Created: 05/04/10 @ 06:08:25 | Last updated: 05/04/10 @ 06:08:26

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 71 times | Downloaded: 46 times

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

Created: 21/07/10 @ 13:16:00 | Last updated: 21/07/10 @ 13:23:12

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 16 times

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

Created: 21/07/10 @ 13:24:56 | Last updated: 01/09/10 @ 17:37:48

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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    

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 14 times

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

Created: 21/07/10 @ 13:56:08 | Last updated: 21/07/10 @ 13:58:41

Credits: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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    

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 26 times | Downloaded: 13 times

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

Created: 21/07/10 @ 14:08:32 | Last updated: 07/09/10 @ 10:04:55

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 19 times

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

Created: 21/07/10 @ 14:21:50 | Last updated: 21/07/10 @ 14:21:52

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 13 times

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

Created: 21/07/10 @ 14:36:36 | Last updated: 01/09/10 @ 17:35:20

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 26 times | Downloaded: 13 times

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Workflow BLAST against the GPCRDB (1)

Created: 24/08/10 @ 13:45:14 | Last updated: 24/08/10 @ 13:45:16

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 54 times | Downloaded: 29 times

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Workflow Create custom-made GPCR alignments (1)

Created: 24/08/10 @ 13:58:32 | Last updated: 24/08/10 @ 13:58:35

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 43 times | Downloaded: 32 times

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Workflow M_Fetch_e-T_phylo_boot - (BETA) (1)

Created: 10/03/10 @ 15:44:02 | Last updated: 10/03/10 @ 15:49:06

Credits: User Achille Zappa User Hamish McWilliam

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 47 times | Downloaded: 19 times

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

Created: 01/09/10 @ 17:16:24 | Last updated: 01/09/10 @ 17:18:45

Credits: User Lebreton

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 38 times | Downloaded: 16 times

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

Created: 01/09/10 @ 17:22:14 | Last updated: 01/09/10 @ 17:22:37

Credits: User Lebreton

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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  

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 15 times

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

Created: 01/09/10 @ 17:26:07 | Last updated: 01/09/10 @ 17:26:39

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

Created: 01/09/10 @ 17:31:29 | Last updated: 01/09/10 @ 17:33:51

Credits: User Lebreton

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 

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Workflow Sff2Fasta_Blast_ParseBlast (1)

Created: 22/09/10 @ 12:40:55 | Last updated: 22/09/10 @ 13:35:26

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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/      

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Workflow Sff2Fasta_Blat (1)

Created: 22/09/10 @ 13:18:55 | Last updated: 22/09/10 @ 13:35:49

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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/  

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Workflow Sff2Fasta_Blast_Blat_ParseBlast (1)

Created: 22/09/10 @ 13:22:57 | Last updated: 22/09/10 @ 13:36:12

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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/  

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Workflow EBI_NCBI_BLAST (1)

Created: 17/01/11 @ 12:51:58 | Last updated: 17/01/11 @ 12:52:03

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs an 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.

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Workflow InterproScan without Looping (1)

Created: 16/03/11 @ 14:01:22 | Last updated: 29/08/12 @ 08:30:44

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow BiomartAndEMBOSSDisease (4)

Created: 27/01/11 @ 17:03:03 | Last updated: 04/09/12 @ 09:32:08

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow DAS sequence retrieval (2)

Created: 30/05/11 @ 01:20:35 | Last updated: 30/05/11 @ 01:26:47

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Workflow DAS sequence retrieval and parsing with JDAS (1)

Created: 30/05/11 @ 03:12:23 | Last updated: 30/05/11 @ 03:14:03

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow DAS features retrieval (2)

Created: 01/06/11 @ 17:10:43 | Last updated: 01/06/11 @ 17:57:45

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Workflow tblastx non-redundant alignment (1)

Created: 30/06/11 @ 15:26:13 | Last updated: 04/07/11 @ 16:51:41

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

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Workflow EBI NCBI BLAST Multi FASTA (2)

Created: 16/07/11 @ 19:08:38 | Last updated: 16/07/11 @ 19:35:11

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow BLAST your sequences against the NucleaRDB (1)

Created: 19/08/11 @ 10:32:03 | Last updated: 19/08/11 @ 10:41:38

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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

Created: 13/08/10 @ 14:02:59 | Last updated: 19/11/10 @ 05:32:37

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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...

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

Created: 19/03/12 @ 11:59:57 | Last updated: 02/04/12 @ 22:51:40

Credits: User Ankit upadhyay

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 1 | Comments: 6 | Citations: 0

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Workflow NCBI Protein Clustal Omega Alignment (1)

Created: 31/08/12 @ 19:18:55

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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