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Items tagged with "similarity" (15)

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Workflows (15)

Taverna 1 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v3) Created: 24/11/09 @ 17:14:43 \| Last updated: 03/12/09 @ 15:28:49 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype. Example input for this workflow is given below (as newline separated values). qt... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 261 times \| Downloaded: 125 times Tags (11): common \| data-driven \| disease \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| similarity	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	BLAST using DDBJ service (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:31:20 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 541 times \| Downloaded: 199 times Tags (5): bioinformatics \| BLAST \| ddbj \| sequence \| similarity	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:28:50 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV... Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 309 times \| Downloaded: 102 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 28/07/09 @ 13:01:45 License: Creative Commons Attribution-No Derivative Works 3.0 Unported 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: 335 times \| Downloaded: 137 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	View Download (v2)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Spectrum similarity search witn SWI-Prolog in Bioclipse (v1) Created: 13/03/10 @ 02:07:23 \| Last updated: 19/03/10 @ 13:15:41 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License With the SWI-Prolog (currently in experimental stage, and available from GitHub) plugin Prolog programs can be accessed inside Bioclipse’s scripting environment for querying and other processing of RDF triples. The prolog code in this Bioclipse script performs a simple spectrum similarity search based on a list of peak shift values, for which it tries to find spectra that contain peaks values close to those values, within a certian limit (<0.3 ppm in this case). The data which is u... Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 28 times \| Downloaded: 18 times Tags (5): bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Taverna 2 Original Uploader wabi	Homology workflow (v1) Created: 12/05/10 @ 07:31:32 \| Last updated: 12/05/10 @ 07:33:11 Credits: wabi License: Creative Commons Attribution-Share Alike 3.0 Unported License There are many kinds of DNA data derived from many species in DDBJ. It makes possible to carry out the comparative study of genes of multiple species. The workflow provides a list of species and their genes that are similar to a human gene in response to a name of the human gene. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 16 times Tags (5): BLAST \| ddbj \| homology \| orthologue \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with In-memory RDF Store (v1) Created: 14/05/10 @ 17:36:38 \| Last updated: 14/05/10 @ 17:43:00 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 7 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with TDB RDF Store (v1) Created: 14/05/10 @ 17:37:47 \| Last updated: 14/05/10 @ 17:43:03 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 14 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Pellet with In-memory RDF Store (v1) Created: 14/05/10 @ 17:38:46 \| Last updated: 14/05/10 @ 17:43:09 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 6 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog (v1) Created: 14/05/10 @ 17:40:14 \| Last updated: 14/05/10 @ 17:43:13 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 12 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog, minimal version (v1) Created: 14/05/10 @ 17:41:04 \| Last updated: 14/05/10 @ 17:42:46 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 12 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Taverna 2 Original Uploader Morgan Taschuk	Extract unique proteins from blast results (v4) Created: 24/03/11 @ 19:49:43 \| Last updated: 01/04/11 @ 12:26:27 Credits: Morgan Taschuk A Team Attributions: Parse unique proteins from Blast file License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 17 times Tags (8): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| tab \| uniqueness	View Download (v4)
Taverna 2 Original Uploader Morgan Taschuk	Drug Re-Purposing Workflow (v6) Created: 25/03/11 @ 20:06:13 \| Last updated: 01/04/11 @ 12:40:56 Credits: Morgan Taschuk A Team License: Creative Commons Attribution-Share Alike 3.0 Unported License The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene... Rating: 0.0 / 5 (0 ratings) \| Versions: 6 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 38 times \| Downloaded: 25 times Tags (7): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| uniqueness	View Download (v6)
Taverna 2 Original Uploader Morgan Taschuk	Threshold BLAST results (v2) Created: 28/03/11 @ 11:57:51 \| Last updated: 01/04/11 @ 12:28:38 Credits: Morgan Taschuk A Team License: Creative Commons Attribution-Share Alike 3.0 Unported License Thresholds tab-delimited BLAST results to a certain percent identity. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 13 times Tags (5): BLAST \| protein \| similarity \| tab-delimited \| threshold	View Download (v2)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI NCBI BLAST Multi FASTA (v2) Created: 16/07/11 @ 19:08:38 \| Last updated: 16/07/11 @ 19:35:11 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 9 times Tags (6): BLAST \| ebi \| FASTA \| fasta format \| sequence \| similarity	View Download (v2)