Workflows

Compare genome, extract proteins which are... (1)

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  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...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

Retrieve Genome Seqn using gi nos (1)

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Retrieves the genome seqn for both the target and source strains using gi nos

Created: 2010-03-19

Credits: Ian Laycock nclteamc

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

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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...

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

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

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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.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

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

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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.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

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

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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.

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

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

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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.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

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

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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.

Created: 2010-04-05 | Last updated: 2011-01-09

Credits: cory (Kazuki Oshita)

EBI_InterProScan for Taverna 2 (2)

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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 s...

Created: 2010-01-26 | Last updated: 2010-01-26

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

EBI_InterProScan for Taverna 2 (2)

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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 t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

Attributions: EBI_InterProScan for Taverna 2 EBI InterproScan T2 EBI_InterProScan EBI InterProScan