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Uploader:

Paul Fisher

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

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

Uploader:

Paul Fisher

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

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: 727 times | Downloaded: 530 times

Uploader:

M.B.Mon...

Workflow for Protein Sequence Analysis (v1)

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

Credits: M.B.Monteiro

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

License: Creative Commons Attribution-Share Alike 3.0 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: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 733 times | Downloaded: 695 times

Uploader:

M.B.Mon...

Workflow for Protein Sequence Analysis (v1)

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

Credits: M.B.Monteiro

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

License: Creative Commons Attribution-Share Alike 3.0 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: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 733 times | Downloaded: 695 times

Uploader:

Hamish McWilliam

Protein_search_fetch_align_tree (v1)

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

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

License: Creative Commons Attribution 3.0 License

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

Viewed: 149 times | Downloaded: 166 times

Uploader:

Hamish McWilliam

EBI WU-BLAST with prompt (v2)

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

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST

License: Creative Commons Attribution 3.0 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.

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

Viewed: 205 times | Downloaded: 139 times

Uploader:

Hamish McWilliam

EBI_NCBI_BLAST_with_prompts (v1)

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

Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 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.

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

Viewed: 125 times | Downloaded: 114 times

Uploader:

Hamish McWilliam

Nucleotide_InterProScan (v3)

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

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: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 205 times | Downloaded: 173 times

Uploader:

Hamish McWilliam

NCBI_QBLAST (v2)

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

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 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: 156 times | Downloaded: 207 times