(C) Copyright Daniel Nilsson, 2002-2005

Please contact Daniel Nilsson, [email protected] with questions and requests.

The use of the program is free for use in research, but please cite Benz, Nilsson, Andersson, Clayton, Gulbride; Messenger processing sites in Trypanosoma brucei, MBP 2005

Usage example:

for file in ../../gbk/*.gbk ; do /home/daniel/bin/splicemodel.improvedpA.pl --infile $file --min-polypy-length 10 --max-polypy-mismatches 1 --report --reportfile report/basename $file .gbk.report --gff gff/basename $file .gbk.gff --gff-utrs utrs_gff/basename $file .gbk.utrs.gff --polypy-ag 261 --5pag-atg 1850 --max-stop-ag-distance 5040 --polya-model center --splitstats --statistics stats/basename $file .gbk.r --rout --min-qual-polypy-run 8 --polya-pyag 100 --half-polya-win 36 --coupled-polya --short >> ../$RUNDIR.cshort.log 2>&1; done

Please do consider as an alternative the use of the SLT technique to experimentally determine the splicesites in your species of choice (Nilsson et al, PLoS Pathogens 2010). See e.g. splicer.unibe.ch.