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Items tagged with "BLAST" (17)

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Workflows (17)

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Workflow BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:13:48

License: Creative Commons Attribution-NoDerivs 3.0 License

Blast_using_ddbj_service_29247
Perform a sequence similarity search using the BLAsT algorithm through the DDBJ web service

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 714 times | Downloaded: 548 times

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Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:14:48

License: Creative Commons Attribution-NoDerivs 3.0 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.

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

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Workflow Simpliy a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:28:07

License: Creative Commons Attribution-NoDerivs 3.0 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 | Updated: 10/01/08 @ 12:09:38

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 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: 0 | Citations: 0

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Workflow Workflow for Protein Sequence Analysis (v1)

Created: 09/01/08 @ 12:03:03 | Updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simpliy a BLAST text file Workflow conditional branch

License: Creative Commons Attribution-Share Alike 3.0 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

Viewed: 733 times | Downloaded: 695 times

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Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:12 | Updated: 06/03/08 @ 17:01:32

License: Creative Commons Attribution-NoDerivs 3.0 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

Viewed: 530 times | Downloaded: 456 times

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Workflow Workflow for Protein Sequence Analysis (v1)

Created: 09/01/08 @ 12:03:03 | Updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simpliy a BLAST text file Workflow conditional branch

License: Creative Commons Attribution-Share Alike 3.0 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

Viewed: 733 times | Downloaded: 695 times

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Workflow EBI_blastpgp_PSI-BLAST (v1)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 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.

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

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Workflow Protein_search_fetch_align_tree (v1)

Created: 31/05/08 @ 21:09:15 | Updated: 31/05/08 @ 21:09:15

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 License

Protein_search_fetch_align_tree_3947_1
An implmentation of the classical sequence analysis workflow: 1. Find homologues (sequence similarity search) 2. Fetch homologues 3. Align homologues (multiple sequence alignment) 4. Produce phylogenetic tree In this implementation the EBI webservices are used: 1. WU-BLAST (WSWUBlast) blastp vs. UniProtKB 2. dbfetch (WSDbfetch) 3. ClustalW (WSClustalW2) 4. ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with ...

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

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Workflow EBI_WU-BLAST (v1)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 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.

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

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Workflow EBI WU-BLAST with prompt (v2)

Created: 30/05/08 @ 22:56:49 | Updated: 02/06/08 @ 21:30:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 License

Ebi_wu-blast_with_prompt_31025_2
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.

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

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Workflow EBI_NCBI_BLAST (v1)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 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.

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

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Workflow EBI_NCBI_BLAST_with_prompts (v1)

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

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 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.

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

Viewed: 125 times | Downloaded: 114 times

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Workflow Retrieve Protein Sequence and BLAST (v1)

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

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 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 (v3)

Created: 06/06/08 @ 21:45:09 | Updated: 07/06/08 @ 09:06:50

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 License

Nucleotide_interproscan_7287_3
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...

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

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Workflow EBI_Blast2InterPro (v1)

Created: 07/06/08 @ 10:52:46 | Updated: 07/06/08 @ 10:52:46

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 License

Ebi_blast2interpro_31843_1
Perform a BLAST search add information about the InterPro matches associated with the hits. This implementation uses: 1. EBI’s WSWUBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/wublast) to perform the initial BLAST search against UniProtKB. 2. 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/int...

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

Viewed: 151 times | Downloaded: 159 times

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Workflow NCBI_QBLAST (v2)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 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.

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

Viewed: 156 times | Downloaded: 207 times

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