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#!/bin/sh
echo ""
echo "STARTING FASTA36" `date` "on" `hostname`
echo `uname -a`
echo ""
if [ ! -d results ]; then
mkdir results
fi
echo "starting prss36(ssearch/fastx)" `date`
../bin/ssearch36 -q -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test_m1.rss
../bin/fastx36 -q -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test_m1.rfx
echo "done"
#echo "starting tfasta36" `date`
#tfasta36 -q ../seq/mgstm1.aa %RMB > results/test_m1.tk2
#echo "done"
echo "starting lalign36" `date`
../bin/lalign36 -k 1000 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal
../bin/lalign36 -z 3 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal_z3
../bin/lalign36 -s BL62 -f -11 -g -1 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal_bl62
../bin/lalign36 -k 1000 -q ../seq/mwkw.aa ../seq/mwkw.aa > results/test_mw.lal
../bin/lalign36 -z 3 -q ../seq/mwkw.aa ../seq/mwkw.aa > results/test_mw.lal_z3
../bin/lalign36 -s BL62 -f -11 -g -1 -q ../seq/mwkw.aa ../seq/mwkw.aa > results/test_mw.lal_bl62
echo "FINISHED" `date`
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