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#!/bin/sh
echo ""
echo "STARTING FASTA36" `date` "on" `hostname`
echo `uname -a`
echo ""
if [ ! -d results ]; then
mkdir results
fi
# export FA_DB=/slib2/fa_dbs/qfo20.lseg
#
# echo "starting fasta36 - protein" `date`
# ../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html
# ../bin/fasta36 -S -q -z 11 -O results/test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 $FA_DB
# echo "done"
# echo "starting fastxy36" `date`
# ../bin/fastx36 -m 9c -S -q ../seq/mgtt2_x.seq $FA_DB 1 > results/test_t2.xk1
# ../bin/fasty36 -S -q ../seq/mgtt2_x.seq $FA_DB > results/test_t2.yk2
# ../bin/fastx36 -m 9c -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.xk2z2
# ../bin/fasty36 -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.yk2z2
# echo "done"
# echo "starting fastxy36 rev" `date`
# ../bin/fastx36 -m 9c -q -m 5 ../seq/mgstm1.rev $FA_DB > results/test_m1.xk2r
# ../bin/fasty36 -q -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz2
# ../bin/fasty36 -q -m 5 -z 11 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz11
# echo "done"
# echo "starting ssearch36" `date`
# ../bin/ssearch36 -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.ssz3
# ../bin/ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.ss_p25
# echo "done"
# if [ -e ../bin/ssearch36s ]; then
# echo "starting ssearch36s" `date`
# ../bin/ssearch36s -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.sssz3
# ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
# echo "done"
# 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 ggsearch36/glsearch36" `date`
# ../bin/ggsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gg
# ../bin/glsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gl
# ../bin/ggsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gg
# ../bin/glsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gl
# echo "done"
# echo "starting fasta36 - DNA" `date`
# ../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
# ../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
# echo "done"
#echo "starting tfasta36" `date`
#tfasta36 -q ../seq/mgstm1.aa %RMB > results/test_m1.tk2
#echo "done"
# echo "starting tfastxy36" `date`
# ../bin/tfastx36 -m 9c -q -i -3 -m 6 ../seq/mgstm1.aa %p > results/test_m1.tx2.html
# ../bin/tfasty36 -q -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test_m1.ty2
# echo "done"
# echo "starting fastf36" `date`
# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff
# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff_s
# echo "done"
# echo "starting tfastf36" `date`
# ../bin/tfastf36 -q ../seq/m1r.aa %r > results/test_mf.tfr
# echo "done"
# echo "starting fasts36" `date`
# ../bin/fasts36 -q -V '*?@' ../seq/ngts.aa $FA_DB > results/test_m1.fs1
# ../bin/fasts36 -q ../seq/ngt.aa $FA_DB > results/test_m1.fs
# ../bin/fasts36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfs
# echo "starting fastm36" `date`
# ../bin/fastm36 -q ../seq/ngts.aa $FA_DB > results/test_m1.fm
# ../bin/fastm36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfm
# echo "done"
# echo "starting tfasts36" `date`
# ../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
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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