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Items tagged with "BLAST" (54)

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Workflows (53)
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

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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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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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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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Original Uploader

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 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 EBI_blastpgp_PSI-BLAST (1)

Created: 31/05/08 @ 14:39:22

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

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

Viewed: 133 times | Downloaded: 65 times

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Workflow Protein_search_fetch_align_tree (2)

Created: 07/04/09 @ 20:13:19

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

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

Viewed: 463 times | Downloaded: 154 times

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Original Uploader

Workflow EBI_WU-BLAST (1)

Created: 30/05/08 @ 22:47:18 | Last updated: 06/12/10 @ 10:51:04

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params. Note: the WSWUBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement WU-BLAST services (REST or SOAP) should be used instead.  

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

Viewed: 234 times | Downloaded: 82 times

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Original Uploader

Workflow EBI WU-BLAST with program and database sel... (3)

Created: 04/07/09 @ 11:39:54 | Last updated: 06/12/10 @ 10:56:44

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me...

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

Viewed: 207 times | Downloaded: 86 times

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Original Uploader

Workflow EBI_NCBI_BLAST (1)

Created: 31/05/08 @ 08:38:46 | Last updated: 06/12/10 @ 10:54:16

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLA...

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

Viewed: 348 times | Downloaded: 166 times

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Original Uploader

Workflow EBI_NCBI_BLAST_with_prompts (1)

Created: 31/05/08 @ 08:40:29 | Last updated: 06/12/10 @ 10:55:09

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 Unported License

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Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...

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

Viewed: 116 times | Downloaded: 77 times

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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 Nucleotide_InterProScan (4)

Created: 26/10/08 @ 21:10:09 | Last updated: 01/04/11 @ 08:54:21

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run InterProScan using a...

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

Viewed: 415 times | Downloaded: 125 times

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Workflow EBI_Blast2InterPro (2)

Created: 26/10/08 @ 20:45:45 | Last updated: 22/08/12 @ 11:22:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST Workflow EBI_dbfetch_fetchBatch Workflow Fasta_string_to_fasta_list Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform a BLAST search a...

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

Viewed: 272 times | Downloaded: 103 times

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Original Uploader

Workflow NCBI_QBLAST (2)

Created: 07/06/08 @ 15:05:00 | Last updated: 07/06/08 @ 17:11:36

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

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

Viewed: 159 times | Downloaded: 80 times

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Original Uploader

Workflow Blast against ENSEMBLE Danio_rerio_Genome (1)

Created: 15/10/08 @ 08:43:51 | Last updated: 15/10/08 @ 09:21:35

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

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

Viewed: 99 times | Downloaded: 142 times

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Workflow BlatBlastCombi (2)

Created: 03/02/09 @ 08:20:43 | Last updated: 03/02/09 @ 08:28:06

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

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

Viewed: 126 times | Downloaded: 60 times

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Workflow blastp using the MRS system (1)

Created: 28/11/08 @ 15:13:32 | Last updated: 28/11/08 @ 15:34:19

Credits: User Bas Vroling

License: Creative Commons Attribution 3.0 Unported License

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

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

Viewed: 89 times | Downloaded: 44 times

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Workflow Multi sequences NCBI BLAST (1)

Created: 05/12/08 @ 02:57:21

Credits: User Whybiocc

Attributions: Workflow EBI_NCBI_BLAST Workflow EBI_NCBI_BLAST_with_prompts Workflow EBI_Blast2InterPro

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Run a BLAST analysis using the EBI's WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence file, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default.

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

Viewed: 143 times | Downloaded: 91 times

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Workflow Mapping OligoNucleotides to an assembly (7)

Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 627 times | Downloaded: 115 times

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Workflow Nucleotide InterProScan for the BioExtract... (3)

Created: 16/04/09 @ 15:26:57 | Last updated: 01/07/09 @ 08:32:34

Credits: User Carol Lushbough User Hamish McWilliam

Attributions: Workflow Nucleotide_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen...

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

Viewed: 158 times | Downloaded: 91 times

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Workflow fetchEnsemblSeqsAndBlast (1)

Created: 18/04/08 @ 11:53:19 | Last updated: 18/04/08 @ 11:58:30

Credits: User Bela

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

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

Viewed: 269 times | Downloaded: 58 times

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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

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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

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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

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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 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

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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 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 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_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 NCBI BLAST (SOAP) (1)

Created: 29/11/10 @ 20:46:58 | Last updated: 29/11/10 @ 20:47:00

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

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Workflow NCBI BLAST (SOAP) (1)

Created: 29/11/10 @ 20:03:13 | Last updated: 29/11/10 @ 20:03:14

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

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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.

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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.

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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 Extract unique proteins from blast results (4)

Created: 24/03/11 @ 19:49:43 | Last updated: 01/04/11 @ 12:26:27

Credits: User Morgan Taschuk Network-member A Team

Attributions: Workflow Parse unique proteins from Blast file

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ...

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Workflow Drug Re-Purposing Workflow (6)

Created: 25/03/11 @ 20:06:13 | Last updated: 01/04/11 @ 12:40:56

Credits: User Morgan Taschuk Network-member A Team

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

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

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Workflow Threshold BLAST results (2)

Created: 28/03/11 @ 11:57:51 | Last updated: 01/04/11 @ 12:28:38

Credits: User Morgan Taschuk Network-member A Team

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Thresholds tab-delimited BLAST results to a certain percent identity.

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Workflow KEGG Pathways and Additional Information f... (2)

Created: 29/03/11 @ 11:16:17 | Last updated: 30/03/11 @ 16:09:01

Credits: User Morgan Taschuk

Attributions: Workflow extract_uniprot_embl_gi.xml

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

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

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Workflow Get names of proteins similar to RNA bindi... (1)

Created: 18/05/11 @ 15:24:56 | Last updated: 18/05/11 @ 15:39:02

Credits: User hindlem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names.

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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 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...

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

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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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Pack Package: mapping oligonucleotides to an assembly


Created: 11/12/08 @ 12:02:47 | Last updated: 22/01/09 @ 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"  

0 items in this pack

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