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Nucleotide_ORF_translation (1)

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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).

Created: 2008-06-06

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

Nucleotide_InterProScan (4)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: Hamish McWilliam

Attributions: EBI_InterProScan EBI_NCBI_BLAST Nucleotide_ORF_translation Fasta_string_to_fasta_list Sequence_or_ID

EBI_CENSOR (2)

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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.

Created: 2008-06-17 | Last updated: 2008-06-25

Credits: Hamish McWilliam

tRNAscan (1)

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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).

Created: 2008-06-28

Credits: Hamish McWilliam

Attributions: Sequence_or_ID_or_GI