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Items tagged with "genome" (11)

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Workflows (11)
Original Uploader

Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:20:58

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 53 times | Downloaded: 23 times

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Original Uploader

Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:24:02

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 57 times | Downloaded: 37 times

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Original Uploader

Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:22:28

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 68 times | Downloaded: 27 times

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Original Uploader

Workflow G-language Genome Analysis Environment - G... (3)

Created: 05/04/10 @ 06:17:25 | Last updated: 09/01/11 @ 06:08:19

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 42 times | Downloaded: 25 times

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Original Uploader

Workflow Run MGCAT for Global Sequence Comparison (1)

Created: 19/03/10 @ 13:42:38

Credits: Network-member Baywatch Solutions

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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Runs the M-GCAT tool for Global Sequence Comparison. M-GCAT: http://alggen.lsi.upc.es/recerca/align/mgcat/ intro-mgcat.html

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

Viewed: 21 times | Downloaded: 22 times

Tags (3):

Original Uploader

Workflow Retrieve Genome Seqn using gi nos (1)

Created: 19/03/10 @ 15:17:53

Credits: User Ian Laycock Network-member nclteamc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 29 times | Downloaded: 12 times

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Original Uploader

Workflow G-language Genome Analysis Environment - B... (2)

Created: 05/04/10 @ 06:08:25 | Last updated: 05/04/10 @ 06:08:26

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta...

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

Viewed: 71 times | Downloaded: 46 times

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Original Uploader

Workflow Virus genome extraction workflow (1)

Created: 13/05/10 @ 01:59:19 | Last updated: 13/05/10 @ 01:59:48

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve genome entries which agree with the following conditions regarding the Definition item of entries from both VRL and PHG division in DDBJ. Includes "complete sequence" or includes "segment" and "complete sequence" Not include "TPA:" and "nearly complete"

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

Viewed: 28 times | Downloaded: 13 times

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Original Uploader

Workflow Phylogenetic Study Using the Bio Extract S... (2)

Created: 17/06/10 @ 16:34:50 | Last updated: 19/07/10 @ 20:00:00

Credits: User Kendra Giesey Network-member BioExtract Server for Genomics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 86 times | Downloaded: 48 times

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Original Uploader

Workflow DAS sequence retrieval (2)

Created: 30/05/11 @ 01:20:35 | Last updated: 30/05/11 @ 01:26:47

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

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

Viewed: 18 times | Downloaded: 7 times

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Original Uploader

Workflow DAS sequence retrieval and parsing with JDAS (1)

Created: 30/05/11 @ 03:12:23 | Last updated: 30/05/11 @ 03:14:03

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

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

Viewed: 15 times | Downloaded: 8 times

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