Mercurial > repos > konradpaszkiewicz > interproscan
diff README.txt @ 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Wed Jun 05 13:40:56 2013 -0400 @@ -0,0 +1,23 @@ +#Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter, UK +Revisions 2013 by Peter Cock, The James Hutton Institute, UK + +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 +similarity. E.g after a denovo transcriptome assembly, each transcript could be translated and run through this tool. + +Prerequisites: + +1. A working installation of Interproscan on your Galaxy server/cluster. + +Limitations: + +Currently it is setup to work with PFAM only due to the heavy computational demands Interproscan makes. + +Input formats: + +The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will of run an ORF +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 +sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant +positional information. + + +