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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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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
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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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6
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7 Prerequisites:
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8
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9 1. A working installation of Interproscan on your Galaxy server/cluster.
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10
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11 Limitations:
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12
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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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14
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15 Input formats:
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16
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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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