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Items tagged with "ddbj" (16)

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Workflows (16)

Taverna 1 Original Uploader Katy Wolstencroft	Retrieve Protein Sequence and BLAST (v1) Created: 09/11/07 @ 10:41:12 \| Last updated: 05/06/08 @ 15:18:07 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 299 times \| Downloaded: 13 times Tags (6): BLAST \| ddbj \| FASTA \| genbank \| protein sequence \| searchsimple	View
Taverna 1 Original Uploader Paul Fisher	BLAST using DDBJ service (v2) 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 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: 579 times \| Downloaded: 213 times Tags (5): bioinformatics \| BLAST \| ddbj \| sequence \| similarity	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLASTP with simplified results returned (v2) 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 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: 322 times \| Downloaded: 106 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Microarray CEL file to candidate pathways (v2) Created: 08/02/08 @ 14:17:23 \| Last updated: 13/02/09 @ 11:29:52 Credits: Paul Fisher Saeedeh License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 272 times \| Downloaded: 5 times Tags (17): affymetrix \| cel \| data-driven \| ddbj \| disease \| entrez \| gene identifier \| genotype \| kegg \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription	View
Taverna 1 Original Uploader Stian Soiland-Reyes	REST access of xml.nig.ac.jp (WABI) (v1) Created: 14/10/08 @ 16:17:58 \| Last updated: 14/10/08 @ 16:39:03 Credits: Stian Soiland-Reyes License: Creative Commons Attribution 3.0 Unported License 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: 178 times \| Downloaded: 54 times Tags (4): ddbj \| http \| rest \| wabi	View Download (v1)
Taverna 2 Original Uploader wabi	Homology workflow (v1) Created: 12/05/10 @ 07:31:32 \| Last updated: 12/05/10 @ 07:33:11 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 43 times \| Downloaded: 21 times Tags (5): BLAST \| ddbj \| homology \| orthologue \| similarity	View Download (v1)
Taverna 2 Original Uploader wabi	Nucleotide frequency workflow (v2) Created: 13/05/10 @ 01:51:22 \| Last updated: 12/11/10 @ 10:30:15 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 22 times Tags (6): ddbj \| frequency \| population \| pubmed \| snp \| variation	View Download (v2)
Taverna 2 Original Uploader wabi	Virus genome extraction workflow (v1) Created: 13/05/10 @ 01:59:19 \| Last updated: 13/05/10 @ 01:59:48 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 19 times \| Downloaded: 11 times Tags (3): ddbj \| genome \| virus	View Download (v1)
Taverna 2 Original Uploader wabi	BLAST-ClustalW workflow (v1) Created: 13/05/10 @ 02:11:12 \| Last updated: 13/05/10 @ 02:12:28 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 49 times \| Downloaded: 30 times Tags (4): 16s ribosomal rna \| BLAST \| clustalw \| ddbj	View Download (v1)
Taverna 2 Original Uploader wabi	BLAST workflow (v1) Created: 13/05/10 @ 02:15:45 \| Last updated: 13/05/10 @ 02:17:34 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 72 times \| Downloaded: 20 times Tags (4): BLAST \| ddbj \| pdb \| swiss-prot	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:10:40 \| Last updated: 21/07/10 @ 13:10:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 17 times \| Downloaded: 10 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| services \| xml	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:16:00 \| Last updated: 21/07/10 @ 13:23:12 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 18 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:16:24 \| Last updated: 01/09/10 @ 17:18:45 Credits: Lebreton Attributions: 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 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: 19 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:22:14 \| Last updated: 01/09/10 @ 17:22:37 Credits: Lebreton Attributions: retrieve protein sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 13 times \| Downloaded: 11 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast (v1) Created: 13/12/10 @ 14:41:12 \| Last updated: 13/12/10 @ 15:15:45 Attributions: BLAST using DDBJ service License: Creative Commons Attribution 3.0 Unported License 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: 12 times \| Downloaded: 9 times Tags (15): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast with concatinated gene id (v1) Created: 13/12/10 @ 14:41:39 \| Last updated: 13/12/10 @ 14:47:55 Attributions: BLAST using DDBJ service Biomart and Blast License: Creative Commons Attribution 3.0 Unported License 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: 13 times \| Downloaded: 11 times Tags (9): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)