Mercurial > repos > konradpaszkiewicz > interproscan
comparison README_INTERPROSCAN @ 1:3c57a8767bb8 draft default tip
Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
| author | peterjc |
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| date | Wed, 05 Jun 2013 13:40:56 -0400 |
| parents | 49e20fa2c66d |
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| 0:49e20fa2c66d | 1:3c57a8767bb8 |
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| 1 #Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter | |
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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 | |
| 4 similarity. E.g after a denovo transcriptome assembly, each transcript could be translated and run through this tool. | |
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| 6 Prerequisites: | |
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| 8 1. A working installation of Interproscan on your Galaxy server/cluster. | |
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| 10 Limitations: | |
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| 12 Currently it is setup to work with PFAM only due to the heavy computational demands Interproscan makes. | |
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| 14 Input formats: | |
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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 | |
| 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 | |
| 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 | |
| 19 positional information. | |
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