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Items tagged with "ddbj" (16)

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Workflows (16)
Original Uploader

Workflow Retrieve Protein Sequence and BLAST (1)

Created: 09/11/07 @ 10:41:12 | Last updated: 05/06/08 @ 15:18:07

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 and then performs a BLAST on that sequence

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

Viewed: 315 times | Downloaded: 13 times

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Original Uploader

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

Tags (5):

Original Uploader

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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Original Uploader

Workflow Microarray CEL file to candidate pathways (2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:52

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) http://www.bioinf.manchester.ac.uk/MADAT/index.html. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ch...

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

Viewed: 296 times | Downloaded: 5 times

Tags (17):

Original Uploader

Workflow REST access of xml.nig.ac.jp (WABI) (1)

Created: 14/10/08 @ 16:17:58 | Last updated: 14/10/08 @ 16:39:03

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data. Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl The example invokes the getDDBJEntry(accession) method of the getE...

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

Viewed: 195 times | Downloaded: 58 times

Tags (4):

Original Uploader

Workflow Homology workflow (1)

Created: 12/05/10 @ 07:31:32 | Last updated: 12/05/10 @ 07:33:11

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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There are many kinds of DNA data derived from many species in DDBJ. It makes possible to carry out the comparative study of genes of multiple species. The workflow provides a list of species and their genes that are similar to a human gene in response to a name of the human gene.

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

Viewed: 50 times | Downloaded: 26 times

Tags (5):

Original Uploader

Workflow Nucleotide frequency workflow (2)

Created: 13/05/10 @ 01:51:22 | Last updated: 12/11/10 @ 10:30:15

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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No description

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

Viewed: 46 times | Downloaded: 23 times

Tags (6):

Original Uploader

Workflow Virus genome extraction workflow (1)

Created: 13/05/10 @ 01:59:19 | Last updated: 13/05/10 @ 01:59:48

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve genome entries which agree with the following conditions regarding the Definition item of entries from both VRL and PHG division in DDBJ. Includes "complete sequence" or includes "segment" and "complete sequence" Not include "TPA:" and "nearly complete"

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

Viewed: 28 times | Downloaded: 13 times

Tags (3):

Original Uploader

Workflow BLAST-ClustalW workflow (1)

Created: 13/05/10 @ 02:11:12 | Last updated: 13/05/10 @ 02:12:28

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Execute blastn against DDBJ database with a given DNA sequence and compare the alignment regions of high similar sequences by using ClustalW.

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

Viewed: 64 times | Downloaded: 34 times

Tags (4):

Original Uploader

Workflow BLAST workflow (1)

Created: 13/05/10 @ 02:15:45 | Last updated: 13/05/10 @ 02:17:34

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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You can get three BLAST results against DDBJ, swiss-prot and PDB by using accession number of DDBJ.

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

Viewed: 82 times | Downloaded: 23 times

Tags (4):

Original Uploader

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

Created: 21/07/10 @ 13:10:40 | Last updated: 21/07/10 @ 13:10:41

Credits: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein 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 : Q9NRA8 database : UNIPROT program : blastp  

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

Viewed: 25 times | Downloaded: 13 times

Tags (6):

Original Uploader

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

Tags (6):

Original Uploader

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

Tags (6):

Original Uploader

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

Tags (6):

Original Uploader

Workflow Biomart and Blast (1)

Created: 13/12/10 @ 14:41:12 | Last updated: 13/12/10 @ 15:15:45

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution 3.0 Unported License

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

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

Viewed: 18 times | Downloaded: 12 times

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Original Uploader

Workflow Biomart and Blast with concatinated gene id (1)

Created: 13/12/10 @ 14:41:39 | Last updated: 13/12/10 @ 14:47:55

Attributions: Workflow BLAST using DDBJ service Workflow Biomart and Blast

License: Creative Commons Attribution 3.0 Unported License

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

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

Viewed: 20 times | Downloaded: 14 times

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