1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
#!/bin/csh -f
echo ""
echo "starting fasta36 - protein" `date` "on" `hostname`
echo `uname -a`
echo ""
fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 q > test_m1.ok2.html
fasta36 -S -q -z 11 -O test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 q
echo "done"
echo "starting fastxy36" `date`
fastx36 -m 9 -S -q ../seq/mgtt2_x.seq q > test_t2.xk2
fasty36 -S -q ../seq/mgtt2_x.seq q > test_t2.yk2
fastx36 -m 9 -S -q -z 2 ../seq/mgstm1.esq a > test_m1.xk2z2
fasty36 -S -q -z 2 ../seq/mgstm1.esq a > test_m1.yk2z2
echo "done"
echo "starting fastxy36 rev" `date`
fastx36 -m 9 -q -m 5 mgstm1.rev q > test_m1.xk2r
fasty36 -q -m 5 -M 200-300 -z 2 mgstm1.rev q > test_m1.yk2rz2
fasty36 -q -m 5 -z 11 mgstm1.rev q > test_m1.yk2rz11
echo "done"
echo "starting ssearch36" `date`
ssearch36 -m 9 -S -z 3 -q mgstm1.aa q > test_m1.ssz3
ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 mgstm1.aa q > test_m1.ss_p25
echo "done"
echo "starting fasta36 - DNA" `date`
fasta36 -q -z 2 mgstm1.seq %RMB 4 > test_m1.ok4z2
fasta36 -q mgstm1.rev %RMB 4 > test_m1.ok4r
echo "done"
echo "starting tfasta36" `date`
tfasta36 -q mgstm1.aa %RMB > test_m1.tk2
echo "done"
echo "starting tfastxy36" `date`
tfastx36 -m 9 -q -i -3 -m 6 mgstm1.aa %p > test_m1.tx2.html
tfasty36 -q -i -3 -N 5000 mgstm1.aa %p > test_m1.ty2
echo "done"
echo "starting fastf36" `date`
fastf36 -q m1r.aa q > test_mf.ff_s
echo "done"
echo "starting tfastf36" `date`
tfastf36 -q -E 0.0001 m1r.aa %r > test_mf.tf_r
echo "done"
echo "starting fasts36" `date`
fasts36 -q n0.aa q > test_m1.fs_s
echo "done"
echo "starting tfasts36" `date`
tfasts36 -q n0.aa %r > test_m1.ts_r
echo "done"
echo "done" `date`
|
