Tag Results

Items tagged with "BLAST" (54)

Note: some items may not be visible to you, due to viewing permissions.

Workflows (53)

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: 323 times \| Downloaded: 106 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) 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 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: 357 times \| Downloaded: 140 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	View Download (v2)
Taverna 1 Original Uploader Kieren Lythgow	Multiple Blastp (v2) Created: 20/11/07 @ 16:58:38 \| Last updated: 10/01/08 @ 12:09:38 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 482 times \| Downloaded: 157 times Tags (4): bioinformatics \| BLAST \| protein \| sequence	View Download (v2)
Taverna 1 Original Uploader M.B.Mon...	Workflow for Protein Sequence Analysis (v1) Created: 09/01/08 @ 12:03:03 \| Last updated: 09/01/08 @ 12:31:27 Credits: M.B.Monteiro Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 1615 times \| Downloaded: 430 times Tags (10): analysis \| BLAST \| homology \| multiple sequence alignment \| phylogenetic tree \| protein \| sequence \| tree \| wpsa	View Download (v1)
Taverna 1 Original Uploader Franck Tanoh	BLASTP with simplified results returned (v2) 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 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: 192 times \| Downloaded: 58 times Tags (3): bioinformatics \| BLAST \| sequence	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_blastpgp_PSI-BLAST (v1) Created: 31/05/08 @ 14:39:22 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 123 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastpgp \| ebi \| ncbi blast \| PSI-BLAST \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License 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: 419 times \| Downloaded: 140 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_WU-BLAST (v1) Created: 30/05/08 @ 22:47:18 \| Last updated: 06/12/10 @ 10:51:04 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 208 times \| Downloaded: 78 times Tags (5): bioinformatics \| BLAST \| ebi \| sequence similarity search \| wu-blast	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI WU-BLAST with program and database selection prompts. (v3) Created: 04/07/09 @ 11:39:54 \| Last updated: 06/12/10 @ 10:56:44 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License 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: 169 times \| Downloaded: 82 times Tags (6): bioinformatics \| BLAST \| ebi \| sequence similarity search \| user_interaction \| wu-blast	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST (v1) Created: 31/05/08 @ 08:38:46 \| Last updated: 06/12/10 @ 10:54:16 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 312 times \| Downloaded: 154 times Tags (6): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST_with_prompts (v1) Created: 31/05/08 @ 08:40:29 \| Last updated: 06/12/10 @ 10:55:09 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution 3.0 Unported License 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: 109 times \| Downloaded: 73 times Tags (7): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search \| user_interaction	View Download (v1)
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 Hamish McWilliam	Nucleotide_InterProScan (v4) Created: 26/10/08 @ 21:10:09 \| Last updated: 01/04/11 @ 08:54:21 Credits: Hamish McWilliam Attributions: EBI_InterProScan EBI_NCBI_BLAST Nucleotide_ORF_translation Fasta_string_to_fasta_list Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License 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: 358 times \| Downloaded: 119 times Tags (11): bioinformatics \| BLAST \| ebi \| interpro \| interproscan \| ncbi blast \| nucleotide sequence \| nucleotide translation \| open reading frame \| protein \| protein annotation	View Download (v4)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Blast2InterPro (v2) Created: 26/10/08 @ 20:45:45 \| Last updated: 01/04/11 @ 08:55:49 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License 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: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 245 times \| Downloaded: 94 times Tags (11): bioinformatics \| BLAST \| dbfetch \| ebi \| go terms \| interpro \| interproscan \| protein \| protein annotation \| sequence similarity search \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	NCBI_QBLAST (v2) Created: 07/06/08 @ 15:05:00 \| Last updated: 07/06/08 @ 17:11:36 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 136 times \| Downloaded: 70 times Tags (5): bioinformatics \| BLAST \| ncbi \| ncbi blast \| sequence similarity search	View Download (v2)
Taverna 1 Original Uploader Wassinki	Blast against ENSEMBLE Danio_rerio_Genome (v1) Created: 15/10/08 @ 08:43:51 \| Last updated: 15/10/08 @ 09:21:35 Credits: Wassinki License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 82 times \| Downloaded: 37 times Tags (1): BLAST	View Download (v1)
Taverna 1 Original Uploader Wassinki	BlatBlastCombi (v2) Created: 03/02/09 @ 08:20:43 \| Last updated: 03/02/09 @ 08:28:06 Credits: Wassinki License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 111 times \| Downloaded: 54 times Tags (3): BLAST \| blat	View Download (v2)
Taverna 1 Original Uploader Bas Vroling	blastp using the MRS system (v1) Created: 28/11/08 @ 15:13:32 \| Last updated: 28/11/08 @ 15:34:19 Credits: Bas Vroling License: Creative Commons Attribution 3.0 Unported License 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: 79 times \| Downloaded: 36 times Tags (4): BLAST \| protein \| similarity search \| xml	View Download (v1)
Taverna 1 Original Uploader Whybiocc	Multi sequences NCBI BLAST (v1) Created: 05/12/08 @ 02:57:21 Credits: Whybiocc Attributions: EBI_NCBI_BLAST EBI_NCBI_BLAST_with_prompts EBI_Blast2InterPro License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 0 \| Citations: 0 Viewed: 123 times \| Downloaded: 85 times Tags (1): BLAST	View Download (v1)
Taverna 1 Original Uploader Wassinki	Mapping OligoNucleotides to an assembly (v7) Created: 13/02/09 @ 09:05:35 \| Last updated: 13/02/09 @ 09:08:20 Credits: Wassinki Pieter Neerincx Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 554 times \| Downloaded: 105 times Tags (7): biomart \| BLAST \| blat \| ensembl \| microarray \| r \| rshell	View Download (v7)
Taverna 1 Original Uploader Aailyso	Identify_strain_and_phylogenetic_tree (v1) Created: 20/03/09 @ 15:20:36 \| Last updated: 20/03/09 @ 15:22:25 Credits: Aailyso Hamish McWilliam AID License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 169 times \| Downloaded: 46 times Tags (6): BLAST \| blast; clustalw \| clustalw \| database \| phylogenetic tree; \| protein	View Download (v1)
BioExtract Server Original Uploader Carol Lushbough	Nucleotide InterProScan for the BioExtract Server (v3) Created: 16/04/09 @ 15:26:57 \| Last updated: 01/07/09 @ 08:32:34 Credits: Carol Lushbough Hamish McWilliam Attributions: Nucleotide_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 149 times \| Downloaded: 89 times Tags (5): bioinformatics \| BLAST \| blastp \| ebi \| interproscan	View Download (v3)
Taverna 1 Original Uploader Bela	fetchEnsemblSeqsAndBlast (v1) Created: 18/04/08 @ 11:53:19 \| Last updated: 18/04/08 @ 11:58:30 Credits: Bela License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 244 times \| Downloaded: 50 times Tags (1): BLAST	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	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 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 BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 13:24:56 \| Last updated: 01/09/10 @ 17:37:48 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 17 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| protein \| sequence \| services	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 nucleotide sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:56:08 \| Last updated: 21/07/10 @ 13:58:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 17 times \| Downloaded: 9 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services (v4) Created: 21/07/10 @ 14:08:32 \| Last updated: 07/09/10 @ 10:04:55 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 28 times \| Downloaded: 16 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v4)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 14:21:50 \| Last updated: 21/07/10 @ 14:21:52 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 9 times \| Downloaded: 10 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 2 Original Uploader Bas Vroling	BLAST against the GPCRDB (v1) Created: 24/08/10 @ 13:45:14 \| Last updated: 24/08/10 @ 13:45:16 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 37 times \| Downloaded: 22 times Tags (4): BLAST \| gpcrdb \| protein \| sequence	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 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:26:07 \| Last updated: 01/09/10 @ 17:26:39 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:31:29 \| Last updated: 01/09/10 @ 17:33:51 Credits: Lebreton Attributions: retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 8 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_ParseBlast (v1) Created: 22/09/10 @ 12:40:55 \| Last updated: 22/09/10 @ 13:35:26 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License 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/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 15 times Tags (9): alignment \| BLAST \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_Blat_ParseBlast (v1) Created: 22/09/10 @ 13:22:57 \| Last updated: 22/09/10 @ 13:36:12 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License 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/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 17 times Tags (10): alignment \| BLAST \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:46:58 \| Last updated: 29/11/10 @ 20:47:00 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 16 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:03:13 \| Last updated: 29/11/10 @ 20:03:14 Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 44 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	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)
Taverna 2 Original Uploader Katy Wolstencroft	EBI_NCBI_BLAST (v1) Created: 17/01/11 @ 12:51:58 \| Last updated: 17/01/11 @ 12:52:03 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 34 times Tags (13): async \| asynchronous services \| BLAST \| blastp \| database \| ebi \| example \| looping \| ncbi \| ncbi blast \| protein sequence \| sequence \| uniprot	View Download (v1)
Taverna 2 Original Uploader Morgan Taschuk	Extract unique proteins from blast results (v4) Created: 24/03/11 @ 19:49:43 \| Last updated: 01/04/11 @ 12:26:27 Credits: Morgan Taschuk A Team Attributions: Parse unique proteins from Blast file License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 46 times \| Downloaded: 22 times Tags (8): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| tab \| uniqueness	View Download (v4)
Taverna 2 Original Uploader Morgan Taschuk	Drug Re-Purposing Workflow (v6) Created: 25/03/11 @ 20:06:13 \| Last updated: 01/04/11 @ 12:40:56 Credits: Morgan Taschuk A Team License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 62 times \| Downloaded: 27 times Tags (7): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| uniqueness	View Download (v6)
Taverna 2 Original Uploader Morgan Taschuk	Threshold BLAST results (v2) Created: 28/03/11 @ 11:57:51 \| Last updated: 01/04/11 @ 12:28:38 Credits: Morgan Taschuk A Team License: Creative Commons Attribution-Share Alike 3.0 Unported License Thresholds tab-delimited BLAST results to a certain percent identity. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 15 times Tags (5): BLAST \| protein \| similarity \| tab-delimited \| threshold	View Download (v2)
Taverna 2 Original Uploader Morgan Taschuk	KEGG Pathways and Additional Information from BLAST (v2) Created: 29/03/11 @ 11:16:17 \| Last updated: 30/03/11 @ 16:09:01 Credits: Morgan Taschuk Attributions: extract_uniprot_embl_gi.xml License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 45 times \| Downloaded: 20 times Tags (6): BLAST \| GO \| interpro \| medline \| pathway \| uniprot	View Download (v2)
Taverna 2 Original Uploader hindlem	Get names of proteins similar to RNA binding proteins (Simple example SADI workflow) (v1) Created: 18/05/11 @ 15:24:56 \| Last updated: 18/05/11 @ 15:39:02 Credits: hindlem License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| GO \| sadi \| uniprot	View Download (v1)
Taverna 2 Original Uploader Bas Vroling	BLAST your sequences against the NucleaRDB (v1) Created: 19/08/11 @ 10:32:03 \| Last updated: 19/08/11 @ 10:41:38 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 5 times Tags (4): BLAST \| nucelardb \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI NCBI BLAST Multi FASTA (v2) Created: 16/07/11 @ 19:08:38 \| Last updated: 16/07/11 @ 19:35:11 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 25 times \| Downloaded: 17 times Tags (6): BLAST \| ebi \| FASTA \| fasta format \| sequence \| similarity	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	KEIO Bioinformatics Web Service - a generating sequence logo image for a set of sequence retrieval via homology search (v2) Created: 13/08/10 @ 14:02:59 \| Last updated: 19/11/10 @ 05:32:37 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 35 times \| Downloaded: 28 times Tags (9): BLAST \| FASTA \| g-language \| kbws \| muscle \| protein \| sequence \| togows \| weblogo	View Download (v2)