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Items tagged with "interproscan" (6)

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_InterProScan (v3)

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

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License

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

Hamish McWilliam

EBI_InterProScan_with_prompts (v1)

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

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

License: Creative Commons Attribution 3.0 License

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

Hamish McWilliam

EBI_InterProScan_tmhmm_signalp (v4)

Created: 01/06/08 @ 11:21:46 | Last updated: 26/10/08 @ 20:50:11

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.

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

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_transmembrane_prediction (v2)

Created: 01/06/08 @ 17:49:32 | Last updated: 26/10/08 @ 21:16:10

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

License: Creative Commons Attribution 3.0 License

Transmembrane and signal peptide prediction using three methods: 1. EMBOSS tmap with a single sequence. Uses Soaplab tmap. 2. Phobius. Uses EBI's WSPhobius web service. 3. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 3 | Citations: 0

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Taverna 1

Original Uploader

Hamish McWilliam

Nucleotide_InterProScan (v4)

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

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 License

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

Hamish McWilliam

EBI_Blast2InterPro (v2)

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

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list EBI_InterProScan

License: Creative Commons Attribution 3.0 License

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

Viewed: 356 times | Downloaded: 344 times

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