Mercurial > repos > konradpaszkiewicz > interproscan
diff README_INTERPROSCAN @ 0:49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 17:27:16 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_INTERPROSCAN Tue Jun 07 17:27:16 2011 -0400 @@ -0,0 +1,22 @@ +#Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter + +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. + + +