User: Ian Laycock

Name: Ian Laycock

Joined: Wednesday 10 March 2010 @ 18:53:41 (GMT)

Last seen: Friday 02 July 2010 @ 11:24:18 (GMT)

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Location: Congo, the Democratic Republic of the

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1 Group (member)

7 Workflows

13 Favourites

Ian Laycock has been credited 9 times

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(1 rating in total)

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Taverna 2 Original Uploader Ian Laycock	Retrieve Genome Seqn using gi nos (v1) Created: 19/03/10 @ 15:17:53 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves the genome seqn for both the target and source strains using gi nos Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 10 times Tags (5): FASTA \| genome \| gi \| nucleotide \| sequence	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Extract proteins from xml blast results (v1) Created: 19/03/10 @ 14:14:44 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The workflow extracts a list of proteins from the target genome that may be known drugs using the blast similarity results. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 9 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Parse unique proteins from Blast file (v1) Created: 19/03/10 @ 14:07:24 \| Last updated: 19/03/10 @ 14:09:22 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 14 times Tags (1): protein	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	blastp of target vs source database (v1) Created: 19/03/10 @ 13:57:32 \| Last updated: 19/03/10 @ 14:05:40 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast License: Creative Commons Attribution-Share Alike 3.0 Unported License This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 18 times Tags (4): blastall \| blastp \| database \| proteins	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Extract proteins using a gi - output as fasta file (v1) Created: 19/03/10 @ 13:54:54 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow uses the gi id to retrieve a xml format of the genbank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein fasta file. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 18 times Tags (2): gi \| proteins	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	NCBI Gi to Kegg Pathways (v1) Created: 19/03/10 @ 13:47:39 \| Last updated: 19/03/10 @ 13:52:45 Credits: Ian Laycock nclteamc Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 32 times Tags (5): bconv \| color \| kegg \| ncbi \| pathway	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Compare genome, extract proteins which are drug targets, apply to KEGG pathway (v1) Created: 19/03/10 @ 13:16:24 \| Last updated: 19/03/10 @ 13:33:53 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga... Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 150 times \| Downloaded: 58 times Tags (7): colour \| FASTA \| gi \| kegg \| pathway \| proteins \| sequence	View Download (v1)