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annotate README_INTERPROSCAN @ 0:0d3deb069781

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author konradpaszkiewicz
date Tue, 07 Jun 2011 16:43:40 -0400
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 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
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 similarity. E.g after a denovo transcriptome assembly, each transcript could be translated and run through this tool.
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 Prerequisites:
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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8 1. A working installation of Interproscan on your Galaxy server/cluster.
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 Limitations:
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 Currently it is setup to work with PFAM only due to the heavy computational demands Interproscan makes.
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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14 Input formats:
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will of run an ORF
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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17 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
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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18 sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant
0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 positional information.
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0d3deb069781 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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