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Items tagged with "interpro" (6)

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Workflows (6)
Taverna 1

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Workflow EBI_InterProScan (v3)

Created: 31/05/08 @ 11:38:58 | Last updated: 26/10/08 @ 20:33:34

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_interproscan
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

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Taverna 1

Original Uploader

Workflow EBI_InterProScan_with_prompts (v1)

Created: 31/05/08 @ 11:40:35

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_with_prompts_27955_1
Run an InterProScan analysis using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). This workflow wraps the EBI_InterProScan workflow to provide a basic user interface which prompts for the required inputs: protien sequence and user e-mail. Other parameters are allowed to default.

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

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Taverna 1

Original Uploader

Workflow Nucleotide_InterProScan (v4)

Created: 06/06/08 @ 21:45:10 | Last updated: 26/10/08 @ 21:10:10

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
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: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow EBI_Blast2InterPro (v2)

Created: 07/06/08 @ 10:52:47 | Last updated: 26/10/08 @ 20:45:46

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
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: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (v2)

Created: 08/06/08 @ 13:53:40 | Last updated: 08/06/08 @ 14:10:04

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

License: Creative Commons Attribution 3.0 License

Ebi_picr_sequence_to_uniparc_and_interpro_23605_2
Given a protein sequence get some information about it: 1. Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. 2. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have th...

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

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Taverna 1

Original Uploader

Workflow EBI_Fetch_InterPro_Matches_UniParc (v1)

Created: 08/06/08 @ 14:08:48

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_fetch_interpro_matches_uniparc_24712_1
For a UniParc (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) identifier/accession fetch the assocated InterPro Matches from SRS@EBI (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC).

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

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