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Items tagged with "nucleotide sequence" (4)

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Workflows (4)
Original Uploader

Workflow Nucleotide_ORF_translation (1)

Created: 06/06/08 @ 20:13:04

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).

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

Viewed: 206 times | Downloaded: 110 times

Tags (8):

Original Uploader

Workflow Nucleotide_InterProScan (4)

Created: 26/10/08 @ 21:10:09 | Last updated: 01/04/11 @ 08:54:21

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run InterProScan using a...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 415 times | Downloaded: 125 times

Tags (11):

Original Uploader

Workflow EBI_CENSOR (2)

Created: 17/06/08 @ 20:42:46 | Last updated: 25/06/08 @ 06:16:03

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 162 times | Downloaded: 51 times

Tags (6):

Original Uploader

Workflow tRNAscan (1)

Created: 28/06/08 @ 09:57:33

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID_or_GI

License: Creative Commons Attribution 3.0 Unported License

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Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE). This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).

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

Viewed: 162 times | Downloaded: 57 times

Tags (6):

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