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Items tagged with "sequence similarity search" (13)

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Workflows (13)

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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_FASTA (v1)

Created: 30/05/08 @ 23:50:46 | Updated: 02/06/08 @ 21:31:18

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_fasta_20674_1
Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).

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

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Workflow EBI FASTA with prompts (v3)

Created: 30/05/08 @ 23:53:16 | Updated: 02/06/08 @ 21:31:41

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA

License: Creative Commons Attribution 3.0 License

Ebi_fasta_with_prompts_25201_3
Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default.

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

Viewed: 198 times | Downloaded: 146 times

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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.

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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 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 Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:29 | Updated: 01/06/08 @ 12:20:29

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 License

Protein_alignment_transmembrane_5019_1
Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3. Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webs...

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

Viewed: 125 times | Downloaded: 124 times

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Workflow EBI_MPsrch (v1)

Created: 02/06/08 @ 21:49:11 | Updated: 02/06/08 @ 21:49:11

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_mpsrch_820_1
Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch).

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

Viewed: 139 times | Downloaded: 102 times

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Workflow EBI_ScanPS (v1)

Created: 03/06/08 @ 05:57:09 | Updated: 03/06/08 @ 05:57:09

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_scanps_5485_1
Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool.

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

Viewed: 121 times | Downloaded: 107 times

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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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