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Items tagged with " sequence" (10)

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Workflows (10)

BioExtract Server

Original Uploader

Carol Lushbough

NCBI tblastx non-redundant alignment (v2)

Created: 18/06/09 @ 19:41:21 | Last updated: 25/02/10 @ 19:40:26

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow may be downloaded and imported into the BioExtract Server at bioextract.org. Once imported, input and/or parameter setting can be easily modified. This workflow executes NCBI tblastx on a sequence provided by the user. It then saves the results as a searchable data extract, executes xmknr to remove duplicate sequences, and performs a clustal alignment on the CDS protein translations.

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

Viewed: 56 times | Downloaded: 76 times

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - Bacteria Analysis System (v1)

Created: 27/06/09 @ 09:10:04 | Last updated: 27/06/09 @ 09:26:24

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 ...

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

Viewed: 19 times | Downloaded: 11 times

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - GC skew analysis (basic) (v1)

Created: 27/06/09 @ 09:13:38 | Last updated: 27/06/09 @ 09:31:22

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 4 times

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - GC skew analysis (sequence retrieval via togoWS) (v1)

Created: 27/06/09 @ 09:14:44 | Last updated: 27/06/09 @ 09:25:36

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - Basic sequence manipulations (v1)

Created: 27/06/09 @ 09:16:23 | Last updated: 27/06/09 @ 09:25:20

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 6 times | Downloaded: 5 times

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - GC skew analysis (multiple) (v1)

Created: 27/06/09 @ 09:18:18 | Last updated: 27/06/09 @ 09:24:42

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 7 times | Downloaded: 9 times

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Taverna 2

Original Uploader

Cory

G-language Genome Analysis Environment - GC skew analysis (AT skew) (v1)

Created: 27/06/09 @ 09:19:10 | Last updated: 27/06/09 @ 09:24:11

Credits: Cory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Taverna 2

Original Uploader

Stian Soiland-Reyes

EBI_InterProScan for Taverna 2 (v2)

Created: 30/06/09 @ 14:06:25 | Last updated: 26/01/10 @ 14:46:09

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

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

Viewed: 68 times | Downloaded: 53 times

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Taverna 2

Original Uploader

Stian Soiland-Reyes

Biomart and EMBOSS analysis (v1)

Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:33

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

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

Viewed: 45 times | Downloaded: 9 times

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Taverna 1

Original Uploader

Achille

M_Fetch_e-T_phylo_boot - (BETA) (v1)

Created: 10/03/10 @ 15:44:02 | Last updated: 10/03/10 @ 15:49:13

Credits: Achille Hamish McWilliam

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

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

Viewed: 7 times | Downloaded: 0 times

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