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Items tagged with "mapping" (7)

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Workflows (7)

Taverna 1 Original Uploader Pierre Lindenbaum	snpNeighbours (v1) Created: 14/05/09 @ 21:03:25 \| Last updated: 14/05/09 @ 21:11:54 Credits: Pierre Lindenbaum License: Creative Commons Attribution-Share Alike 3.0 Unported License My first Taverna workflow: the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 92 times \| Downloaded: 44 times Tags (4): genomics \| mapping \| snp \| web services	View Download (v1)
LONI Pipeline Original Uploader Pipeline	mrFAST Indexing and Mapping (v1) Created: 05/04/11 @ 21:47:48 \| Last updated: 05/04/11 @ 21:48:54 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License This page contains a number of bioinformatics workflows based on the mrFAST sequence analysis package. This page describes Pipeline bioinformatics modules from the mrFAST suite. mrFAST (micro-read Fast Alignment Search Tool) is mapper designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 6 bp. This manu... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 5 times Tags (4): alignment \| mapping \| mrfast \| pipeline	View Download (v1)
LONI Pipeline Original Uploader Pipeline	Integrated Mapping and Assembly with Qualities (MAQ), SAMtools, Bowtie Workflow (v1) Created: 05/04/11 @ 22:05:03 \| Last updated: 05/04/11 @ 22:05:11 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow contains the first step of a genomics data analysis protocol designed and implemented by Federica Torri, Fabio Macciardi and Ivo Dinov to process large number of sequence data outputted by the Illumina sequencing pipeline. See Step II analysis (GATK/QC/Cleaning) here. This protocol is implemented using the LONI Pipeline environment and includes the following types of computational resources: Mapping and Assembly with Qualities (MAQ) Sequence Alignment and Mapping t... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 70 times \| Downloaded: 24 times Tags (8): assembly \| bowtie \| interoperability \| mapping \| maq \| pipeline \| qualities \| samtools	View Download (v1)
LONI Pipeline Original Uploader Pipeline	Direct Hippocampal Mapping (v1) Created: 06/04/11 @ 01:35:39 \| Last updated: 06/04/11 @ 01:35:45 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License Overview - Direct Hippo Mapping The workflow takes volumetric masks of hippocampi from two groups, generates surfaces from each mask, and maps these surfaces to a hippocampal atlas. It also computes thickness and displacement feature on the surfaces and evaluates the statistical significance of the differences between the two groups with respect to these measurements. Problem addressed by this workflow Automatically establishing correspondences between points on hippocampal ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 5 times Tags (6): brain \| brain imaging \| direct \| hippocampus \| mapping \| surface	View Download (v1)
Taverna 2 Original Uploader Dennis Leenheer	[untitled] (v1) Created: 26/04/11 @ 14:50:37 \| Last updated: 26/04/11 @ 15:04:28 Credits: Dennis Leenheer License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 9 times Tags (16): bioinformatics \| biosemantics \| datamining \| global test \| GO \| kegg \| literature weighted global test \| mapping \| normalization \| rma \| sommation \| taverna \| taverna 2 \| textmining \| weighted global test \| workflow	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI PICR, find cross-references for protein accessions (v2) Created: 18/05/11 @ 09:36:26 \| Last updated: 29/05/11 @ 17:35:20 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 9 times Tags (5): cross-references \| ebi \| mapping \| picr \| protein accessions	View Download (v2)
Taverna 2 Original Uploader Paul martin	Define Associated Regions and Genes (v2) Created: 08/02/12 @ 16:08:08 \| Last updated: 09/05/12 @ 09:52:18 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 13 times Tags (14): association \| disease \| disease-associated genes \| ensembl \| gene \| genes \| genome wide association studies \| gwas \| mapping \| ncbi \| ngs \| sequencing \| snp \| ucsc	View Download (v2)