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
48
49
50
51
52
53
54
|
#!/bin/sh
echo "#----------------------------------------------------------------------#"
echo "# pftools test 1: pfsearch -f sh3.prf sh3.seq C=6.0"
echo "#----------------------------------------------------------------------#"
pfsearch -f sh3.prf sh3.seq C=6.0
echo "#----------------------------------------------------------------------#"
echo "# pftools test 2: pfsearch -bx ecp.prf CVPBR322 | psa2msa -du"
echo "#----------------------------------------------------------------------#"
pfsearch -bx ecp.prf CVPBR322 | psa2msa -du
echo "#----------------------------------------------------------------------#"
echo "# pftools test 3: pfscan -s GTPA_HUMAN prosite13.prf"
echo "#----------------------------------------------------------------------#"
pfscan -s GTPA_HUMAN prosite13.prf
echo "#----------------------------------------------------------------------#"
echo "# pftools test 4: pfscan -by CVPBR322 ecp.prf L=2"
echo "#----------------------------------------------------------------------#"
pfscan -by CVPBR322 ecp.prf L=2
echo "#----------------------------------------------------------------------#"
echo "# pftools test 5: gtop sh3.gpr F=50 | pfsearch -far - sh3.seq"
echo "# | sort -nr"
echo "#----------------------------------------------------------------------#"
gtop sh3.gpr F=50 | pfsearch -far - sh3.seq | sort -nr
echo "#----------------------------------------------------------------------#"
echo "# pftools test 6: htop pfam_sh3.hmm | pfsearch -f - sh3.seq"
echo " | sort -nr"
echo "#----------------------------------------------------------------------#"
htop pfam_sh3.hmm | pfsearch -f - sh3.seq | sort -nr
echo "#----------------------------------------------------------------------#"
echo "# pftools test 7: pfw sh3.msf N=1000 |"
echo "# pfmake -b - blosum45.cmp H=0.6"
echo "#----------------------------------------------------------------------#"
pfw sh3.msf N=1000 | pfmake -b - blosum45.cmp H=0.6
echo "#----------------------------------------------------------------------#"
echo "# pftools test 8: ptoh ecp.prf L=1.15"
echo "#----------------------------------------------------------------------#"
ptoh ecp.prf L=1.15
echo "#----------------------------------------------------------------------#"
echo "# pftools test 9: pfscale score.lis N=14147368 P=0.0001"
echo "# Q=0.000001 | sed -n 1,25p"
echo "#----------------------------------------------------------------------#"
pfscale score.lis N=14147368 P=0.0001 Q=0.000001 | sed -n 1,25p
echo "#----------------------------------------------------------------------#"
echo "# pftools test 10: pfsearch -y coils.prf MYSA_HUMAN"
echo "#----------------------------------------------------------------------#"
pfsearch -y coils.prf MYSA_HUMAN
echo "#----------------------------------------------------------------------#"
echo "# pftools test 11: rm sh3.fsp"
echo "# ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 >sh3.fsp"
echo "# 2ft < R76849.seq | pfsearch -fy sh3.fsp - C=5.0"
echo "# rm sh3.fsp"
echo "#----------------------------------------------------------------------#"
rm sh3.fsp; ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 > sh3.fsp ; 2ft < R76849.seq | pfsearch -fy sh3.fsp - C=5.0; rm sh3.fsp
|
