rem "" rem "starting fasta34_t - protein on win32" rem "" fasta34_t -q -m 6 -Z 100000 mgstm1.aa:1-100 q > test_m1.ok2_t.html fasta34_t -S -q -z 11 -O test_m1.ok2_t_p25 -s P250 mgstm1.aa:100-218 q rem "done" rem "starting fastxy34_t" fastx34_t -m 9c -S -q mgtt2_x.seq q 1 > test_t2.xk1_t fasty34_t -S -q mgtt2_x.seq q > test_t2.yk2_t fastx34_t -m 9c -S -q -z 2 mgstm1.esq a > test_m1.xk2_tz2 fasty34_t -S -q -z 2 mgstm1.esq a > test_m1.yk2_tz2 rem "done" rem "starting fastxy34_t rev" fastx34_t -m 9c -q -m 5 mgstm1.rev q > test_m1.xk2r_t fasty34_t -q -m 5 -M 200-300 -z 2 mgstm1.rev q > test_m1.yk2r_tz2 fasty34_t -q -m 5 -z 11 mgstm1.rev q > test_m1.yk2rz11_t rem "done" rem "starting ssearch34_t" ssearch34_t -m 9c -S -z 3 -q mgstm1.aa q > test_m1.ss_tz3 ssearch34_t -q -M 200-300 -z 2 -Z 100000 -s P250 mgstm1.aa q > test_m1.ss_t_p25 rem "starting ssearch34_t" ssearch34sse2_t -m 9c -S -z 3 -q mgstm1.aa q > test_m1.ss_tz3sse2 ssearch34sse2_t -q -M 200-300 -z 2 -Z 100000 -s P250 mgstm1.aa q > test_m1.ss_t_p25sse2 rem "done" rem "starting prss34" prss34_t -q -k 1000 -A mgstm1.aa xurt8c.aa > test_m1.rss prfx34_t -q -k 1000 -A mgstm1.esq xurt8c.aa > test_m1.rfx rem "done" rem "starting fasta34_t - DNA" fasta34_t -S -q -z 2 mgstm1.seq %M 4 > test_m1.ok4_tz2 fasta34_t -S -q mgstm1.rev %M 4 > test_m1.ok4r_t rem "done" rem "starting tfastxy34_t" tfastx34_t -m 9c -q -i -3 -m 6 mgstm1.aa m > test_m1.tx2_t.html tfasty34_t -q -i -3 -N 5000 mgstm1.aa m > test_m1.ty2_t rem "done" rem "starting fastf34_t" fastf34_t -q m1r.aa q > test_mf.ff_t fastf34 -q m1r.aa q > test_mf.ff_s rem "done" rem "starting tfastf34_t" tfastf34_t -q m1r.aa %m > test_mf.tf_tr rem "done" rem "starting fasts34_t" fasts34_t -q -V '*?@' ngts.aa q > test_m1.fs1_t fasts34_t -q ngt.aa q > test_m1.fs_t fasts34_t -q -n mgstm1.nts m > test_m1.nfs_t rem "done" rem "starting tfasts34_t" tfasts34_t -q n0.aa %m > test_m1.ts_r rem "done" rem "starting fasta34 - protein" fasta34 -q -z 2 mgstm1.aa q 1 > test_m1.ok1z2 fasta34 -q -s P250 mgstm1.aa q > test_m1.ok2_p25 rem "done" rem "starting fastx3" fastx34 -m 9c -q mgstm1.esq q > test_m1.ok2x rem "done" rem "starting fasty3" fasty34 -q mgstm1.esq q > test_m1.ok2y rem "done" rem "starting fasta34 - DNA " fasta34 -m 9c -q mgstm1.seq M 4 > test_m1.ok4 rem "done" rem "starting ssearch3" ssearch34 -S -q -z 2 mgstm1.aa a > test_m1.ss_z2 ssearch34 -q -s P250 mgstm1.aa a > test_m1.ss_p25 ssearch34 -S -q -s BL50 mgstm1.aa a > test_m1.ss_bl50 ssearch34 -S -q -s blosum50.mat mgstm1.aa a > test_m1.ss_bl50f ssearch34sse2 -S -q -z 2 mgstm1.aa q > test_m1.ss_z2_sse2 ssearch34sse2 -q -s P250 mgstm1.aa q > test_m1.ss_p25_sse2 rem "done" rem "starting tfastxy3" tfastx34 -q mgstm1.aa M > test_m1.tx2 tfasty34 -m 9c -q mgstm1.aa M > test_m1.ty2 rem "done" rem "starting fasts34" fasts34 -q -V '@?*' ngts.aa q > test_m1.fs1 fasts34 -q ngt.aa q > test_m1.fs rem "done"