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Items tagged with "BLAST" (39)

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Packs (1)

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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"  

5 items in this pack

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Workflows (38)

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Workflow 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

Blast_using_ddbj_service_29247
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

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Workflow 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

Blastp_with_simplified_results_returned_28648
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

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Workflow 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

Simpliy_a_blast_text_file_23463
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

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Workflow Multiple Blastp (v2)

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

Multiple_blastp_7288_2
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

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Workflow Workflow for Protein Sequence Analysis (v1)

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

Workflow_for_protein_sequence_analysis_5539_1
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: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow 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

Blastp_with_simplified_results_returned_14277
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

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Workflow EBI_blastpgp_PSI-BLAST (v1)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Ebi_blastpgp_psi-blast_11519_1
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.

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Workflow Protein_search_fetch_align_tree (v2)

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

Protein_search_fetch_align_tree
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...

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Workflow EBI_WU-BLAST (v1)

Created: 30/05/08 @ 22:47:18 | Last updated: 02/06/08 @ 21:30:17

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Ebi_wu-blast_31786_1
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.

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Workflow EBI WU-BLAST with program and database selection prompts. (v3)

Created: 04/07/09 @ 11:39:54

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

Ebi_wu-blast_with_program_and_database_selection_prompts
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...

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Workflow EBI_NCBI_BLAST (v1)

Created: 31/05/08 @ 08:38:46 | Last updated: 02/06/08 @ 21:32:21

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Ebi_ncbi_blast_8105_1
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.

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Workflow EBI_NCBI_BLAST_with_prompts (v1)

Created: 31/05/08 @ 08:40:29 | Last updated: 02/06/08 @ 21:32:48

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 Unported License

Ebi_ncbi_blast_with_prompts_25022_1
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.

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Workflow Retrieve Protein Sequence and BLAST (v1)

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

Retrieve_protein_sequence_13844
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

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Workflow Nucleotide_InterProScan (v4)

Created: 26/10/08 @ 21:10:09

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

Nucleotide_interproscan
Run InterProScan using a nucleotide sequence as input. 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 Gene Ontology terms. Since InterProScan is a protein search tool to use it with a nucleotide sequence, the sequence must be translated into a protein sequence. There are a number of ways of...

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Workflow EBI_Blast2InterPro (v2)

Created: 26/10/08 @ 20:45:45

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

Ebi_blast2interpro
Perform a BLAST search add information about the InterPro matches associated with the hits. This implementation uses: EBI’s WSWUBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/wublast) to perform the initial BLAST search against UniProtKB. EBI’s WSDbfetch web service (http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) to retreive the sequences of the hits found by BLAST. 3. EBI’s WSInterProScan web service (http://www.ebi.ac.uk/Tools/webservices/services/interp...

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Workflow NCBI_QBLAST (v2)

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

Ncbi_qblast_32544_2
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.

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Workflow Blast against ENSEMBLE Danio_rerio_Genome (v1)

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

Blast
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...

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Workflow BlatBlastCombi (v2)

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

Blatblastcombi
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 ...

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Workflow blastp using the MRS system (v1)

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

Blastp_using_the_mrs_system
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.

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Workflow Multi sequences NCBI BLAST (v1)

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

Multi_sequences_ncbi_blast
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.

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Workflow Mapping OligoNucleotides to an assembly (v7)

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

Mapping_oligonucleotides_to_an_assembly
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. ...

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Workflow Identify_strain_and_phylogenetic_tree (v1)

Created: 20/03/09 @ 15:20:36 | Last updated: 20/03/09 @ 15:22:25

Credits: User Aailyso User Hamish McWilliam Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Whole
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Workflow Nucleotide InterProScan for the BioExtract Server (v3)

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

Interproscan
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...

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Workflow fetchEnsemblSeqsAndBlast (v1)

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

Fetchensemblseqsandblast_12435_1
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...

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Workflow Homology workflow (v1)

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

Homology_workflow
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.

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Workflow BLAST-ClustalW workflow (v1)

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

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

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Workflow BLAST workflow (v1)

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

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

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Workflow 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: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_uniprot_searchparallelblast_extract
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

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Workflow 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: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_uniprot_searchparamblast
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    

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Workflow 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: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_uniprot_searchsimpleblast_extract
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  

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Workflow 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: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_ddbj_searchsimpleblast_extract
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    

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Workflow retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services (v1)

Created: 21/07/10 @ 14:08:32 | Last updated: 21/07/10 @ 14:08:34

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_ddbj_searchparralelblast_extract
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 accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

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Workflow 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: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Getfasta_ddbj_searchparamblast
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

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Workflow BLAST against the GPCRDB (v1)

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.

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Workflow 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: 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

Workflowsemanticm
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

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Workflow 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: 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

Retrieve_protein_sequence_and_do_a_blast_from_ddbj_web_services
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  

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Workflow 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: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieve_nucleotide_sequence_and_do_a_high_speed_blast_from_ddbj_web_services
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 BLAST from DDBJ Web services (v1)

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

Retrieve_nucleotide_sequence_and_do_a_blast_from_ddbj_web_services_
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

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