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Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
author peterjc
date Wed, 05 Jun 2013 13:40:56 -0400
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3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
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1 #Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter, UK
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2 Revisions 2013 by Peter Cock, The James Hutton Institute, UK
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3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
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4 The attached is a crude wrapper script for Interproscan. Typically this is useful when one wants to produce an annotation which is not based on sequence
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
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5 similarity. E.g after a denovo transcriptome assembly, each transcript could be translated and run through this tool.
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7 Prerequisites:
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9 1. A working installation of Interproscan on your Galaxy server/cluster.
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11 Limitations:
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13 Currently it is setup to work with PFAM only due to the heavy computational demands Interproscan makes.
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15 Input formats:
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17 The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will of run an ORF
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18 prediction tool. However this tends to lose the ORF information (e.g. start/end co-ordinates) from the header. As such the requirement here is to input ORF
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19 sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant
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20 positional information.
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