PROANALYST

EXAMPLES WITH STEP-BY-STEP INSTRUCTIONS

COPYRIGHT (C) 1996 Vladimir A.Ivanisenko, Alexey M.Eroshkin

Theoretical Dept., Research Institute of Molecular Biology,
SRC VB "Vector", 633159, Koltsovo, Novosibirsk region, Russia

Examples list:

1. Investigation of relationships between physico-chemical properties of
peptides and their antimicrobial activity by multiple regression
analysis.

2. Simulation of peptide engineering experiments and prediction of
antimicrobial activities of mutants.

3. Searching for activity-modulating sites in disintegrins by profile
analysis.

4. Investigation of relationships between influenza a virus resistance
to rimantadine  and physico-chemical properties of M2 protein by
discriminant analysis.

5. Searching for important functional or structural 3D sites in
alpha-interferons by profile analysis.

6. Searching for patterns in combinatorial peptide library.

7. Profiles of physico-chemical properties (example with Hopp-Woods
hydrophilicity).

NOTE: Calculations were made on the complete program version.

Step-by-step instructions for:

1. INVESTIGATION OF RELATIONSHIPS BETWEEN PHYSICO-CHEMICAL PROPERTIES OF
PEPTIDES AND THEIR ANTIMICROBIAL ACTIVITY BY MULTIPLE REGRESSION
ANALYSIS.

1.  Go to item "File".
2.  Go to the item "Property".
3.  Select the file "Property.ppt".
4.  Press "Alt I" to select all properties and press "Esc".
5.  Go to the item "Protein".
6.  Select the file "Antimicr.ali".
7.  Press "Alt I" to select all peptides and press "Esc".
8.  Go to the item "Prep. data".
9.  Move cursor to the first position in alignment and press "Alt B".
10. Move cursor to the last position in alignment and press "Alt E".
11. Press "F10" or "Esc" to go to the main menu.
12. Go to the item "Options".
13. Go to the item "Calculation".
14. Select "Min frame". Press "Enter", type 23, press "Enter".
15. Select "Max frame". Press "Enter", type 23, press "Enter".
16. Select "Min num. of factors". Press "Enter", type 2, press "Enter".
17. Select "Max num. of factors". Press "Enter", type 2, press "Enter".
18. Go to the main menu (by pressing "Esc").
19. Go to the item "Analysis".
20. Select "Factors definition" and press "Enter".
21. Press "Enter" on the line "Fragment 1 pos. 1-23".
22. Select "Average for a fragment" and press "Enter".
23. Switch all the properties to "On" (by pressing "Enter").
24. Press "Esc" and select "Moment, alpha helix periodicity" then press
    "Enter".
25. Switch all properties to "On"  (by pressing "Enter").
26. Return back to the menu item "Analysis" (by pressing "Esc").
27. Go to the item "Structure-Activity".
28. Select "Multiple regression analysis" and press "ENTER".
29. Select "Automatic" and press "Enter".
30. Wait for calculation. The menu items "Analysis" will be shown
    after calculation finishing.
31. Go to the item "View last result" to see the table of results.
32. Select any result and press "F3" to see the details.
33. To write this result to disk press "F2" and select the name of
    already existing file or type new filename.
34. Press "F5" to view structure-activity plots or press "F6" to
    view the plot of theoretical versus experimental activities.
35. Go to the item "Save last result" (by pressing "Esc") to save
    the whole table of the results.

36. Output of detail result:
_____________________________________________
 Multiple regression analysis.

 Split fragments:  1-23, 1-23,
Gaps - ignore.
 Min-max frame:          28-28
 Min-max number factors: 2-2

 1) 1-23:Hydropathy Kyte-Doolittle ,Average for a fragment

 2) 1-23:HPLC  Parker ,Moment, A-helix periodicity

   N Group Act_e  Act_t  e-t  Value_factors     Name sequence
   1.   1   0.05   0.06  -0.01   0.08   2.05  Magainin 2
   2.   1   0.02  -0.01   0.03  -0.21   2.01  Antisense P
   3.   1   0.01  -0.01   0.02  -0.24   2.04  Analog A1
   4.   1   0.00   0.02  -0.01  -0.11   2.03  Analog A2
   5.   1   0.03  -0.01   0.03  -0.49   2.19  Analog B1
   6.   1   0.03   0.02   0.01  -0.36   2.18  Analog B2
   7.   1   0.05   0.06  -0.01  -0.60   2.48  Analog C1
   8.   1   0.05   0.09  -0.04  -0.47   2.47  Analog C2
   9.   1   0.10   0.16  -0.06  -0.03   2.43  Analog P1
  10.   1   0.20   0.20  -0.00   0.18   2.43  Analog P2
  11.   1   0.20   0.18   0.02  -0.24   2.61  Analog P3
  12.   1   0.40   0.37   0.03   0.13   2.94  Analog M1
  13.   1   0.33   0.33   0.00  -0.12   3.00  Analog M2

   N Group  Alignment sequence:

   1.    1 GIGKFLHSAKKFGKAFVGEIMNS
   2.    1 GIHYLSHKSFSKFFCGVQKFTNS
   3.    1 GIHYLSHKSFSKFFAGVQKFTNS
   4.    1 GIHYLSHKSFSKFFAGVGKFTNS
   5.    1 GIHYLSHKSFSKFFKGVQKFTNS
   6.    1 GIHYLSHKSFSKFFKGVGKFTNS
   7.    1 GIHKLSHKSFSKFFKGVQKFTNS
   8.    1 GIHKLSHKSFSKFFKGVGKFTNS
   9.    1 AIHNFAHKSFAKFFRAVKKFANA
  10.    1 AIHNLAHKSLAKLLRAVKKLANA
  11.    1 GIHNFAHKSFAKFFRAVKKFANS
  12.    1 AIHNLAHKLLKKLLRAVKKLANA
  13.    1 KIHKLAHKLLKKLLKAVKKLAKA

 Y=+ 0.198 X1+ 0.329 X2-0.631
95% confidence intervals for coefficients of regression
           K1     K2     K0
Lower     0.115    0.268   -0.781
High      0.282    0.391   -0.481
 t-test statistics for H0
          5.321   11.960    9.348
 P-values for H0
          0.956    0.994    0.988
 F-test statistic for H0 = 99.547780
 P-value          for H0 = 1.00000
 Multiple correlation coefficient      R=0.975795
 Coefficient of multiple determination R-square=95.217%
 Total variance of activities = 0.017141
 Residual mean squares        = 0.000984

__________________________________________________

37. Common table of results (the upper part):
__________________________________________________
 Multiple regression analysis.
__ Number item: 0 __
 Statistic 99.547780  Sign 1.00000
 Fragments: 1-23 1-23
 Factors:
 1):Hydropathy Kyte-Doolittle ,Average for a fragment
 1):HPLC  Parker ,Moment, A-helix periodicity
__ Number item: 1 __
 Statistic 85.821807  Sign 0.999999
 Fragments: 1-23 1-23
 Factors:
 1):Polarity Grantham,Average for a fragment
 1):HPLC  Parker ,Moment, A-helix periodicity
__ Number item: 2 __
 Statistic 77.788728  Sign 0.999999
 Fragments: 1-23 1-23
 Factors:
 1):Hydropathy Kyte-Doolittle ,Moment, A-helix periodicity
 1):Polarity Bogardt et al.,Average for a fragment
__ Number item: 3 __
 Statistic 70.647806  Sign 0.999999
 Fragments: 1-23 1-23
 Factors:
 1):Hydropathy Kyte-Doolittle ,Moment, A-helix periodicity
 1):HPLC  Parker ,Average for a fragment
__ Number item: 4 __
 Statistic 67.409267  Sign 0.999998
 Fragments: 1-23 1-23
 Factors:
 1):HPLC  Parker ,Average for a fragment
 1):HPLC  Parker ,Moment, A-helix periodicity
__ Number item: 5 __
 Statistic 60.843946  Sign 0.999997
 Fragments: 1-23 1-23
 Factors:
 1):Hydropathy Kyte-Doolittle ,Moment, A-helix periodicity
 1):Hydrophilicity Hopp-Woods,Average for a fragment
__ Number item: 6 __
 Statistic 60.693755  Sign 0.999997
 Fragments: 1-23 1-23
 Factors:
 1):Polarity Grantham,Average for a fragment
 1):Polarity Grantham,Moment, A-helix periodicity
..........
__________________________________________________________________



2. SIMULATION OF PEPTIDE ENGINEERING EXPERIMENTS AND PREDICTION OF
ANTIMICROBIAL ACTIVITIES OF MUTANTS.

1.  Go to the item "File".
2.  Go to the item "Property".
3.  Select file "Property.ppt".
4.  Press "Alt I" to select all properties and press "Esc".
5.  Go to the item "Protein".
6.  Select file "Antimicr.ali".
7.  Press "Alt I" to select all peptides and press "Esc".
8.  Go to the item "Prep. data".
9.  Return back to the item "File".
10. Select the item "Save protein".
11. Type new file name (for example "antimic1").
12. Go to the item "Prep data".
13. Press "Ctrl Alt C" (group's numbers will be changed to 0 for all
    peptides).
14. Move cursor to the first peptide and press "ENTER" (group number of
    the peptide will be changed to 1).
15. Press "ENTER" on the next two peptides. We'll mutate the first
    three peptides.
16. Move cursor to first peptide and press "Alt N".
17. Press "F4".
18. Delete old name by pressing "DEL" and type new name of the peptide
    (for example "mutant1") and press "ENTER".
19. Change the names of the next two peptides (mutant2, mutant3).
20. Press "Esc" to go to the main window.
21. Press "Alt D" to go to activities window.
22. Select mutant1, press "F4", delete old value of activity, type "0",
    press "ENTER".
23. Change the activities of the mutants mutant2 and mutant3..
24. Press "Esc" to go to the main window.
25. Move cursor to position number 8 in mutant1.
26. Type new amino acids "kll". Move cursor to position 12 and type
    "kl".
27. Move cursor to mutant2 and make the same mutations.
28. Make the same mutations in mutant3.
29. Go to the item "File" and select "Save protein".
30. Select file "ANTIMIC1.ALI" and press "ENTER" (peptides with group
    number not equaled to 0 will be added to the file "ANTIMIC1.ALI").
31. Select menu item "Protein".
32. Select file "ANTIMIC1.ALI"
33. Go to the item "Prep. data".
34. Move cursor to "mutant1" and press "ENTER" to change number of
    group to 0).

[This is important. Proteins (peptides) from group "0" will not
be used in calculation of regressions, but theoretical activity
will be calculated for them].

35. Change the number of group to 0 for "mutant2" and "mutant3".
36. Move cursor to the first position in sequence and press "Alt B".
37. Move cursor to the last position in sequence and press "Alt E".
38. Press "F10" or "Esc" to go to the main menu.
39. Go to menu item "Options".
40. Go to the item "Calculation".
41. Select "Min frame". Press "Enter", type 23, press "Enter".
42. Select "Max frame". Press "Enter", type 23, press "Enter".
43. Select "Min num. of factors". Press "Enter", type 2, press "Enter".
44. Select "Max num. of factors". Press "Enter", type 2, press "Enter".
45. Go to the main menu by pressing "Esc".
46. Go to menu item "Analysis".
47. Select "Factors definition".
48. Press "Enter" to select "Fragment 1 pos. 1-23".
49. Select "Average for a fragment".
50. Switch all the properties to "On" by pressing "Enter".
51. Press "Esc" , select "Moment, alpha helix periodicity" and press
    "Enter".
52. Switch all the properties to "On" by pressing "Enter".
53. Return back to the menu item "Analysis" (by pressing "Esc").
54. Go to the item "Structure-Activity".
55. Select "Multiple regression analysis" and press "ENTER".
56. Select "Automatic" and press "Enter".
57. After finishing calculation, menu item "Analysis" will be shown.
58. Go to the item "View last result", press "Enter" and you'll see the
    table of results.
59. Select the first one and press "F3" to view the details.
60. Press "F2" and type the name of result file "resmut1" to write the
    result to disk.
61. You will find the values of theoretical activity for our mutants
    in the file "RESMUT1.RES".

62. RESMUT1.RES listing:
_____________________________________________


 Multiple regression analysis.

 Split fragments:  1-23, 1-23,
Gaps - ignore.
 Min-max frame:          28-28
 Min-max number factors: 2-2

 1) 1-23:Hydropathy Kyte-Doolittle ,Average for a fragment

 2) 1-23:HPLC  Parker ,Moment, A-helix periodicity

   N Group Act_e  Act_t  e-t  Value_factors     Name sequence
   1.   1   0.05   0.06  -0.01   0.08   2.05  Magainin 2
   2.   1   0.02  -0.01   0.03  -0.21   2.01  Antisense P
   3.   1   0.01  -0.01   0.02  -0.24   2.04  Analog A1
   4.   1   0.00   0.02  -0.01  -0.11   2.03  Analog A2
   5.   1   0.03  -0.01   0.03  -0.49   2.19  Analog B1
   6.   1   0.03   0.02   0.01  -0.36   2.18  Analog B2
   7.   1   0.05   0.06  -0.01  -0.60   2.48  Analog C1
   8.   1   0.05   0.09  -0.04  -0.47   2.47  Analog C2
   9.   1   0.10   0.16  -0.06  -0.03   2.43  Analog P1
  10.   1   0.20   0.20  -0.00   0.18   2.43  Analog P2
  11.   1   0.20   0.18   0.02  -0.24   2.61  Analog P3
  12.   1   0.40   0.37   0.03   0.13   2.94  Analog M1
  13.   1   0.33   0.33   0.00  -0.12   3.00  Analog M2
  14.   0   0.00   0.53  -0.53   0.26   3.36 Mutant1
  15.   0   0.00   0.14  -0.14   0.07   2.31 Mutant2
  16.   0   0.00   0.15  -0.15   0.04   2.34 Mutant3

   N Group  Alignment sequence:

   1.    1 GIGKFLHSAKKFGKAFVGEIMNS
   2.    1 GIHYLSHKSFSKFFCGVQKFTNS
   3.    1 GIHYLSHKSFSKFFAGVQKFTNS
   4.    1 GIHYLSHKSFSKFFAGVGKFTNS
   5.    1 GIHYLSHKSFSKFFKGVQKFTNS
   6.    1 GIHYLSHKSFSKFFKGVGKFTNS
   7.    1 GIHKLSHKSFSKFFKGVQKFTNS
   8.    1 GIHKLSHKSFSKFFKGVGKFTNS
   9.    1 AIHNFAHKSFAKFFRAVKKFANA
  10.    1 AIHNLAHKSLAKLLRAVKKLANA
  11.    1 GIHNFAHKSFAKFFRAVKKFANS
  12.    1 AIHNLAHKLLKKLLRAVKKLANA
  13.    1 KIHKLAHKLLKKLLKAVKKLAKA
  14.    0 GIGKFLHkllKklKAFVGEIMNS
  15.    0 GIHYLSHkllSklFCGVQKFTNS
  16.    0 GIHYLSHKllSklFAGVQKFTNS

 Y=+ 0.198 X1+ 0.329 X2-0.631
95% confidence intervals for coefficients of regression
           K1     K2     K0
Lower     0.115    0.268   -0.781
High      0.282    0.391   -0.481
 t-test statistics for H0
          5.321   11.960    9.348
 P-values for H0
          0.956    0.994    0.988
 F-test statistic for H0 = 99.547780
 P-value          for H0 = 1.00000
 Multiple correlation coefficient      R=0.975795
 Coefficient of multiple determination R-square=95.217%
 Total variance of activities = 0.017141
 Residual mean squares        = 0.000984

63. Calculated antimicrobial activity of our mutants are:
0.53  - Mutant1
0.14  - Mutant2
0.15  - Mutant3

__________________________________________________________________



3. SEARCHING FOR ACTIVITY-MODULATING SITES IN DISINTEGRINS BY PROFILE
ANALYSIS.


1.  Go to the item  "File".
2.  Go to the item  "Protein".
3.  Select file "DE1.ALI".
4.  Press "Alt I" to select all proteins and press "Esc".
5.  Go to the item "Prep. data".
6.  Move cursor to the first position and press "Alt B".
7. Move cursor to the last position and press "Alt E".
8. Press "F10" or "Esc" to go to the main menu.
9. Go to the item "Options".
10. Go to the item "Calculation".
11. Select "Min frame". Press "Enter", type 1, press "Enter".
12. Select "Max frame". Press "Enter", type 1, press "Enter".
13. Go to the main menu (press "Esc").
14. Go to the item "Analysis".
15. Go to the item "Structure-Activity".
16. Go to the item "Profile analysis".
17. Go to the item "Alphabetical analysis".
18. Select "SADC    1D" and press "ENTER".
19. Select matrix of amino acids similarity "ONE.MAT" and press "ENTER".
20. Type "0" (threshold value) and press "ENTER".
21. Wait for a moment. The resulting profile will be shown when
    calculation will be complete.
22. Press "F2" if you want to print the profile, otherwise press "Esc".
23. Go to the item "Save profile", select name of already existing file or
    type new name if you want to save the profile to disk.
24. If protein 3D structure is loaded, you can map the profile on 3D
    structure:
25. Go to the item "View profile on    3D".
26. Type upper threshold for low values of the profile and press "ENTER".
27. Type low threshold for high values of the profile and press "ENTER".
28. You'll get stereo picture of protein in three colors that reflects
    the low, intermediate and high values of the profile (low values
    are in RED, intermediate values are in YELLOW and high values
    are in CYAN).
29. Positions of high values are good candidates to activity-modulating
center.

34. Output with profile  to the disk:
_________________________________________________________________


 Current group: SADC

 Value threshold to discriminate clusters: 0.000000 Smoothing 0
Matrix of aa similarity:
matrix


 Fragments:  1-45,
 Min-max frame: 1-1
   N Group     Name sequence
   1.    1    Halysin
   2.    1    Trigramin beta 1
   3.    1    Trigramin alpha
   4.    1    Trigramin gamma
   5.    1    Bitistatin
   6.    1    Albolabrin
   7.    1    Trigramin beta 2
   8.    1    Kistrin
   9.    1    Barbourin
  10.    1    Elegantin
  11.    1    Batroxastatin
  12.    1    Triflavin
  13.    1    Tergemenin
  14.    1    Applagin
  15.    1    Flavoridin
  16.    1    Bitan alpha

   N Group      Aligned sequences:

   1.    1 QCAEGLCCDQCRFMKKGTVCRIARGDDMDDYCNGISAGCPRNPF-
   2.    1 QCGEGPCCDQCSFMKKGTICRRARGDDLDDYCNGRSAGCPRNPFH
   3.    1 QCGEGLCCDQCSFIEEGTVCRIARGDDLDDYCNGRSAGCPRNPFH
   4.    1 QCGEGLCCDQCSFMKKGTICRRARGDDLDDYCNGISAGCPRNPLH
   5.    1 QCNHGECCDQCKFKKARTVCRIARGDWNDDYCTGKSSDCPWNH--
   6.    1 QCGEGLCCDQCSFMKKGTICRRARGDDLDDYCNGISAGCPRNPLH
   7.    1 QCGEGPCCDQCSFMKKGTICRRARGDDLDDYCNGRSAGCPRNPFH
   8.    1 QCGEGLCCEQCKFSRAGKICRIPRGDMPDDRCTGQSADCPRYH--
   9.    1 QCADGLCCDQCRFNKKGTVCRMAKGDWNDDTCTGQSADCPRNGLY
  10.    1 QCADGLCCDQCRFKKKRTICRRARGDNPDDRCTGQSADCPRNGLY
  11.    1 QCAEGLCCDQCRFKGAGKICRRARGDNPDDRCTGQSADCPRNRF-
  12.    1 QCADGLCCDQCRFKKKRTICRIARGDFPDDRCTGQSADCPRWNGL
  13.    1 QCADGLCCDQCRFNKKGTVCRMARGDWNDDTCTGQSADCPRNGLY
  14.    1 QCAEGLCCDQCLFMKEGTVC-RARGDDVNDYCNGISAGCPRNPFH
  15.    1 QCADGLCCDQCRFKKKTGICRIARGDFPDDRCTGLSNDCPRWNDL
  16.    1 QCNHGECCDQCRFKKAGTVCRIARGDWNDDYCTGKSSDCPWNH--

 Value profile:
     1      2      3      4      5      6      7      8      9     10
 0.000  0.000 28.538 28.113  0.000  9.961  0.000  0.000  0.000  0.000

    11     12     13     14     15     16     17     18     19     20
 0.000 45.270  0.000 28.975  5.946  2.857 29.393 28.941  0.074  0.000

    21     22     23     24     25     26     27     28     29     30
19.607  2.676  0.000  0.024  0.000  0.000 40.306 73.580 19.607  0.000

    31     32     33     34     35     36     37     38     39     40
26.959  0.000 26.568  0.000 47.810  0.000 28.123 26.568  0.000  0.000

    41     42     43     44     45
 0.000 27.072 41.209 35.369 34.059
__________________________________________________________________



4. INVESTIGATION OF RELATIONSHIPS BETWEEN INFLUENZA A VIRUS RESISTANCE
TO RIMANTADINE  AND PHYSICO-CHEMICAL PROPERTIES OF M2 PROTEIN BY
DISCRIMINANT ANALYSIS.

1.  Go to the item "File".
2.  Go to the item "Property".
3.  Select file "Property.ppt".
4.  Press "Alt I" to select all properties and press "Esc".
5.  Go to the item "Protein".
6.  Select file "M2.ALI".
7.  Press "Alt I" to select all proteins and press "Esc".
8.  Go to the item "Prep. data".
9.  Move cursor to the first protein with activity 0. Press "Ctrl Alt 2".
    Switch number of group to 2 for all proteins with activity 0
    by pressing "ENTER".
10. Move cursor to the first position in sequence and press "Alt B".
11. Move cursor to the last position and press "Alt E".
12. Press "F10" or "Esc" to go to the main menu.
13. Go to the item "Options".
14. Go to the item "Calculation".
15. Select "Min frame". Press "Enter", type "7", press "Enter".
16. Select "Max frame". Press "Enter", type "7", press "Enter".
17. Select "Min num. of factors". Press "Enter", type "1", press "Enter".
18. Select "Max num. of factors". Press "Enter", type "1", press "Enter".
19. Go to the main menu (by pressing "Esc").
20. Go to the item "Analysis".
21. Select "Factors definition" and press "Enter".
22. Press "Enter" to select "Fragment 1 pos. 1-97".
23. Select "Average for a fragment" and press "Enter".
24. Switch all properties to "On" (by pressing "Enter").
25. Return back to the menu item "Analysis" (by pressing "Esc").
26. Go to the item "Structure-Activity".
27. Select "Discriminant analysis" and press "ENTER".
28. Select "Automatic" and press "Enter".
29. Wait for calculation. After finishing the menu item "Analysis" will
    be shown.
30. Go to the item "View last result" to see the table of results.
31. Select some result and press "F3" to view the details.
32. Press "F2" and select the name of existing file or type new
    name (if you want to write this result to disk).
33. Go to the item "Save last result" (by pressing "Esc") if you want to
    save the table of results.

34. Output with  detail result:
_____________________________________________


 Discr. analysis.

 Split fragments:
Gaps - ignore.
 Min-max frame:          98-98
 Min-max number factors: 1-1

 1) 28-34:Polarity Grantham,Average for a fragment

   N Group Act    Value_factors  Value_Disc_function   Name sequence
   1.   1   1.00   7.49   1.20   PR8-34 r=1
   2.   1   1.00   7.49   1.20   mon88   r
   3.   1   1.00   7.49   1.20   LEN3-83 r
   4.   1   1.00   7.49   1.20   MOS88   r
   5.   1   1.00   7.49   1.20   MON86   r
   6.   1   1.00   7.49   1.20   SVER82  r
   7.   1   1.00   7.49   1.20   WS33    r
   8.   1   1.00   7.59   1.90   LEN85   r
   9.   1   1.00   7.49   1.20   WSN33   r
  10.   1   1.00   7.59   1.90   LEN49   r
  11.   1   1.00   7.24  -0.50   LEN6-83 r
  12.   1   1.00   7.56   1.70   SWONT81 r
  13.   1   1.00   7.56   1.70   SW29-37 r
  14.   1   1.00   7.56   1.70   SWIA30  r
  15.   1   1.00   7.56   1.70   SWWIS61 r
  16.   1   1.00   7.24  -0.50   SWIA88  r
  17.   1   1.00   7.56   1.70   WIS88   r
  18.   1   1.00   7.56   1.70   SWMAR52 r
  19.   1   1.00   7.56   1.70   SWMAY54 r
  20.   1   1.00   7.56   1.70   SWTN77  r
  21.   1   1.00   7.63   2.20   EQPR56  r
  22.   2   0.00   7.24  -0.50   VIC72   s 0
  23.   2   0.00   7.24  -0.50   AICHI   s
  24.   2   0.00   7.24  -0.50   UDORN72 s
  25.   2   0.00   7.24  -0.50   PC73    s
  26.   2   0.00   7.24  -0.50   SING57  s
  27.   2   0.00   7.24  -0.50   AA60    s
  28.   2   0.00   7.24  -0.50   KOREA68 s
  29.   2   0.00   7.24  -0.50   BANG79  s
  30.   2   0.00   7.24  -0.50   FW50    s
  31.   2   0.00   7.24  -0.50   MEM88   s
  32.   2   0.00   7.24  -0.50   USSR77  s
  33.   2   0.00   7.14  -1.20   PINALB79s
  34.   2   0.00   7.14  -1.20   SWHK82  s
  35.   2   0.00   7.14  -1.20   SWNED85 s
  36.   2   0.00   7.14  -1.20   FPVR34  s
  37.   2   0.00   7.14  -1.20   MLRDNY78s
  38.   2   0.00   7.14  -1.20   TYMN81  s
  39.   2   0.00   7.14  -1.20   TYMN80  s
  40.   2   0.00   7.14  -1.20   CKVIC85 s
  41.   2   0.00   7.14  -1.20   FPVD27  s
  42.   2   0.00   7.14  -1.20   DKCZ56  s
  43.   2   0.00   7.14  -1.20   FPVW27  s
  44.   2   0.00   7.14  -1.20   GULMA80 s
  45.   2   0.00   7.14  -1.20   GULMD79 s
  46.   2   0.00   7.14  -1.20   BUDHOK77s
  47.   2   0.00   7.14  -1.20   EQKY86  s
  48.   2   0.00   7.14  -1.20   GULMD78 s
  49.   2   0.00   7.14  -1.20   CKPEN1-83s
  50.   2   0.00   7.14  -1.20   EQTN86   s
  51.   2   0.00   7.14  -1.20   CKPENO-83s

   N Group  Alignment sequence:

   1.    1 IAANIIG
   2.    1 IAANIIG
   3.    1 IAANIIG
   4.    1 IAANIIG
   5.    1 IAANIIG
   6.    1 IAANIIG
   7.    1 IAANIIG
   8.    1 VAANIIG
   9.    1 IAANIIG
  10.    1 VAANIIG
  11.    1 VAASIIG
  12.    1 AAASIIG
  13.    1 AAASIIG
  14.    1 AAASIIG
  15.    1 AAASIIG
  16.    1 AVASIIG
  17.    1 AAASIIG
  18.    1 AAASIIG
  19.    1 AAASIIG
  20.    1 AAASIIG
  21.    1 AIASITG
  22.    2 VAASIIG
  23.    2 VAASIIG
  24.    2 VAASIIG
  25.    2 VAASIIG
  26.    2 VAASIIG
  27.    2 VAASIIG
  28.    2 VAASIIG
  29.    2 VAASIIG
  30.    2 VAASIIG
  31.    2 VAASIIG
  32.    2 VAASIIG
  33.    2 IAASIIG
  34.    2 IAASIIG
  35.    2 IAASIIG
  36.    2 IAASIIG
  37.    2 IAASIIG
  38.    2 IAASIIG
  39.    2 IAASIIG
  40.    2 IAASIIG
  41.    2 IAASIIG
  42.    2 IAASIIG
  43.    2 IAASIIG
  44.    2 IAASIIG
  45.    2 IAASIIG
  46.    2 IAASIIG
  47.    2 IAASIIG
  48.    2 IAASIIG
  49.    2 IAASIIG
  50.    2 IAASIIG
  51.    2 IAASIIG

 _____Mean values______
 Variables/Groups
 7.506122  7.179524
 Function  Eigen values  Ratio (%)  R (Canonical correlation %) R^2
    1     5.065847     100.000000     91.386135     83.514257

_______Discriminant function coefficients _______
 N      0
  -51.198039
  7.000000
_______Standardized coefficients _______
  0.510004
 Structural coefficients (Pearson's correlation coefficients)
  1.000000
____________ Lamda-statistic Uilks  ( critical values)_
   Function     Uilks       Chi-square       Freedom      95%     99%
      1          0.165      87.430          1.000      3.841     6.635

_________________________________________________

35. Output with the table of results (upper part):

 Discriminant analysis.
__ Number item: 0 __
 Statistic 0.164857  Sign 0.000000
 Fragments: 28-34
 Factors:
 1):Polarity Grantham,Average for a fragment
__ Number item: 1 __
 Statistic 0.189363  Sign 0.000000
 Fragments: 28-34
 Factors:
 1):Polarity Bogardt et al.,Average for a fragment
__ Number item: 2 __
 Statistic 0.191667  Sign 0.000000
 Fragments: 28-34
 Factors:
 1):Hydropathy Kyte-Doolittle ,Average for a fragment
__ Number item: 3 __
 Statistic 0.248677  Sign 0.000000
 Fragments: 27-33
 Factors:
 1):Polarity Grantham,Average for a fragment
__ Number item: 4 __
 Statistic 0.256571  Sign 0.000000
 Fragments: 27-33
 Factors:
 1):Polarity Bogardt et al.,Average for a fragment
__ Number item: 5 __
 Statistic 0.279247  Sign 0.000000
 Fragments: 28-34
 Factors:
 1):Hydrophobicity Eisenberg,Average for a fragment
.......................
__________________________________________________________________


5. SEARCHING FOR IMPORTANT FUNCTIONAL OR STRUCTURAL 3D SITES IN
ALPHA-INTERFERONS BY PROFILE ANALYSIS.


1.  Go to the item  "File".
2.  Go to the item  "Protein".
3.  Select file "IFN.ALI".
4.  Press "Alt I" to select all proteins and press "Esc".
5.  Go to the item "Options".
6. Go to the item "Calculation".
7. Select "Type of input atoms". Switch on "CA".
8. Select "Min frame". Press "Enter", type "1", press "Enter".
9. Select "Max frame". Press "Enter", type "1", press "Enter".
10. Select "Cutoff radius" and type "7".
11. Go to the item  "File".
12. Select "3D-Structure".
13. Select file "IFN.PDB", press "Enter"  and select "Complete str".
14. Go to the item "Prep. data".
15.  Move cursor to the first position and press "Alt B".
16.  Move cursor to the last position and press "Alt E".
17.  Press "F10" or "Esc" to go to the main menu.
18. Go to the item "Analysis".
19. Go to the item "Structure-Activity".
20. Go to the item "Profile analysis".
21. Go to the item "Alphabetical analysis".
22. Select "Variation in current group 3D" and press "ENTER".
23. Select matrix of amino acids similarity "ONE.MAT" and press "ENTER".
24. Wait for a moment. The profile will be shown when calculation will
    be finished.
25. Press "F2" if you want to print the profile, otherwise press "Esc".
26. Go to the item "Save profile", select the name from existing files or
    type new name to save profile to disk.
27. If protein 3D structure is loaded, you can map the profile on 3D
    structure:
28. Go to the item "View profile on    3D".
29. Type upper threshold for low values of the profile and press "ENTER".
30. Type low threshold for high values of the profile and press "ENTER".
31. You'll get stereo picture of protein in three colors that reflects
    the low, intermediate and high values of the profile (low values
    are in RED, intermediate values are in YELLOW and high values
    are in CYAN).
32. 3D sites with low profile values are good candidates to
    functional and/or structural important centers.

33. Output with profile result:
_________________________________________________________________


 3D-Structure.
 Variation in current group.
 Cutoff radius 7.000000
 Filter for atoms 1
 Smoothing 0
Matrix of aa similarity:
matrix


 Fragments:  1-164,
 Min-max frame: 1-1
   N Group     Name sequence
   1.    1    MO B pr.
   2.    1    BO B-3 pr.
   3.    1    BO B-2 pr.
   4.    1    BO B-1 pr.
   5.    1    HO B-I pr.
   6.    1    HU B-1 pr.
   7.    1    BO A-II-1 pr.
   8.    1    HO A-II-1 pr.
   9.    1    HO A-II-2 pr.
  10.    1    HU A-II-1 pr.
  11.    1    RA A-I-1 pr.
  12.    1    MO A-I-4 pr.
  13.    1    MO A-2 pr.
  14.    1    MO A-I-6 pr.
  15.    1    MO A-1 pr.
  16.    1    MO A-I-5 pr.
  17.    1    BO A-I-A pr.
  18.    1    BO A-I-C pr.
  19.    1    BO A-I-B pr.
  20.    1    BO A-I-D pr.
  21.    1    BO A-I-1 pr.
  22.    1    HO A-I-1 pr.
  23.    1    HO A-I-3 pr.
  24.    1    HO A-I-2 pr.
  25.    1    HO A-I-4 pr.
  26.    1    HU A-I-8 pr.
  27.    1    HU A-4 pr.
  28.    1    HU A-I-16 pr.
  29.    1    HU A-10 pr.
  30.    1    HU A-9 pr.
  31.    1    HU A-I-4B pr.
  32.    1    HU A-5 pr.
  33.    1    HU A-I-F pr.
  34.    1    HU A-I-14 pr.
  35.    1    HU A-2 pr.
  36.    1    HU A-1 pr.
  37.    1    HU A-I-6 pr.

   N Group      Aligned sequences:

   1.    1 YKQLQLQERTNIRKCQELLEQLNGKI--NLTYRADFKIPMEMTEKMQ--KSYTAFAIQEM
   2.    1 YSLLRFQQRRSAEVCQKLLGQLHSTPQHCLEAKMDFQVPEEMNQAQQFRKEDAILVIYEM
   3.    1 YSLLRFQQRRSLALCQKLLRQLPSTPQHCLEARMDFQMPEEMKQAQQFQKEDAILVIYEM
   4.    1 YSLLRFQQRQSLKECQKLLGQLPSTSQHCLEARMDFQMPEEMKQEQQFQKEDAILVMYEV
   5.    1 YDLLRSQLRSSNSACLMLLRQLNGAPQRCPEDTMNFQVPEEIEQAQQFQKEDAALVIYEM
   6.    1 YNLLGFLQRSSNFQCQKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQFQKEDAALTIYEM
   7.    1 CDLSPNHVLVGRQNLRLLGQMRRLSPRFCLQDRKDFAFPQEMVEVSQFQEAQAISVLHEM
   8.    1 CDLPASLDLRKQETLRVLHQMETISPPSCLKHRTDFRFPQEQLDGRQFPEAQATSVLQEM
   9.    1 CDLPQNHILVSRKNFVLLGQMSRISSAICLKDRKDFRFPQDMADGRQFPEAQAASVLHEM
  10.    1 CDLPQNHGLLSRNTLVLLHQMRRISPFLCLKDRRDFRFPQEMVKGSQLQKAHVMSVLHEM
  11.    1 CDLPHTHNLRNKRVFTLLAQMRRLSPVSCLKDRKYFGFPLEKVDGQQIQKAQAIPVLHEL
  12.    1 CDLPHTYNLGNKRALTVLEEMRRLPPLSCLKDRKDFGFPLEKVDNQQIQKAQAILVLRDL
  13.    1 CDLPHTYNLRNKRALKVLAQMRRLPFLSCLKDRQDFGFPLEKVDNQQIQKAQAIPVLRDL
  14.    1 CDLPQTHNLRNKRALTLLVKMRRLSPLSCLKDRKDFGFPQEKVGAQQIQEAQAIPVLTEL
  15.    1 CDLPQTHNLRNKRALTLLVQMRRLSPLSCLKDRKDFGFPQEKVDAQQIKKAQAIPVLSEL
  16.    1 CDLPQTHNLRNKRALTLLVKMRRLSPLSCLKDRKDFGFPQEKVGAQQIQEAQAIPVLSEL
  17.    1 CHLPHTHSLANRRVLMLLQQLRRVSPSSCLQDRNDFEFLQEALGGSQLQKAQAISVLHEV
  18.    1 CHLPHTHSLANRRVLMLLGQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  19.    1 CHLPHTHSLPNRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  20.    1 CHLPHSHSLAKRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  21.    1 CHLPHSHSLAKRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  22.    1 CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  23.    1 CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  24.    1 CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  25.    1 CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  26.    1 CDLPQTHSLGNRRALILLAQMRRISPFSCLKDRHDFEFPQEEFDDKQFQKAQAISVLHEM
  27.    1 CDLPQTHSLGNRRALILLAQMRRISPFSCLKDRHDFEFPQEEFDDKQFQKAQAISVLHEM
  28.    1 CDLPQTHSLGNRRALILLAQMGRISHFSCLKDRYDFGFPQEVFDGNQFQKAQAISAFHEM
  29.    1 CDLPQTHSLRNRRALILLAQMGRISPFSCLKDRHEFRFPEEEFDGHQFQKTQAISVLHEM
  30.    1 CDLPQTHSLGNRRALILLAQMGRISPFSCLKDRPDFGLPQEEFDGNQFQKTQAISVLHEM
  31.    1 CDLPQTHSLGNRRALILLAQMGRISHFSCLKDRHDFGFPEEEFDGHQFQKTQAISVLHEM
  32.    1 CDLPQTHSLGNRRALILLGQMGRISPFSCLKDRHDFRIPQEEFDGNQFQKAQAISVLHEM
  33.    1 CDLPQTHSLGNRRALILLAQMGRISPFSCLKDRHDFGFPQEEFDGNQFQKAQAISVLHEM
  34.    1 CNLSQTHSLNNRRTLMLMAQMRRISPFSCLKDRHDFEFPQEEFDGNQFQKAQAISVLHEM
  35.    1 CDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEF-GNQFQKAETIPVLHEM
  36.    1 CDLPETHSLDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEFDGNQFQKAPAISVLHEL
  37.    1 CDLPQTHSLGHRRTMMLLAQMRRISLFSCLKDRHDFRFPQEEFDGNQFQKAEAISVLHEV

   1.    1 LQNVFLVFRNNFSSTGWNETIVVRLLDELHQQTVFLKTVL-EEKQEERLTWEMSSTALHL
   2.    1 LQQIFNILTRDFSSTGWSETIIEDLLVELYGQMNRLQPIQKEIMQEQNFTMGDTTV-LHL
   3.    1 LQQIFNILTRDFSSTGWSETIIEDLLEELYEQMNHLEPIQKEIMQKQNSTMGDTTV-LHL
   4.    1 LQHIFGILTRDFSSTGWSETIIEDLLKELYWQMNRLQPIQKEIMQKQNSTTEDTIV-PHL
   5.    1 LQHTWRIFRRNFASTGWNETIVKNLLVEVHLQMDRLETNLEEIMEEESSTWGNTTI-LRL
   6.    1 LQNIFAIFRQDSSSTGWNETIVENLLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHL
   7.    1 LQQSFNLFHKERSSAAWDTTLLEQLLTGLHQQLDDLDACLGLLTGEEDSALGRTGPTLAM
   8.    1 LQQIVSLFHTERSSAAWNTTLLDRLLAGLHQQLEDLNTCLDEQTGEEESALGTVGPTLAV
   9.    1 LQQIFSLFHTERSSAAWNTTLLDELCTGLLRQLEDLDTCLEQEMGEEESALGTVRPTLAV
  10.    1 LQQIFSLFHTERSSAAWNMTLLDQLHTELHQQLQHLETCLLQVVGEGESAGAISSPALTL
  11.    1 TQQILSLFTSKESSTAWDATLLDSFCNDLQQQLSGLQACLMQQVGVQESPLTQEDSLLAV
  12.    1 TQQILNLFTSKDLSATWNATLLDSFCNDLHQQLNDLKACVM-----QEPPLTQEDSLLAV
  13.    1 TQQTLNLFTSKASSAAWNATLLDSFCNDLHQQLNDLQTCLMQQVGVQEPPLTQEDALLAV
  14.    1 TQQILTLFTSKDSSAAWNATLLDSFCNDLHQLLNDLQGCLMQQVEIQALPLTQEDSLLAV
  15.    1 TQQILNIFTSKDSSAAWNATLLDSFCNDLHQQLNDLQGCLMQQVGVQEFPLTQEDALLAV
  16.    1 TQQVLNIFTSKDSSAAWNATLLDSFCNEVHQQLNDLKACVMQQVGVQESPLTQEDSLLAV
  17.    1 TQHTFQLFSTEGSPATWDKSLLDKLRAALDQQLTDLQACLTQEEGLRGAPLLKEDSSLAV
  18.    1 TQHTFQLFSTEGSATMWDESLLDKLRDALDQQLTDLQFCLRQEEELQGAPLLKEDSSLAV
  19.    1 TQHTFQLFSTEGSATTWDESLLDKLHAALDQQLTDLQACLRQEEGLRGAPLLKEGSSLAV
  20.    1 TQHTFQLSSTEGSAAVWDESLLDKLRTALDQQLTDLQACLRQEEGLPGAPLLKEDSSLAV
  21.    1 TQHTFQLFSTEGSAAVWDESLLDRLRTALDQQLTDLQACLRQEEGLPGAPLLKEDSSLAV
  22.    1 IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  23.    1 IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  24.    1 IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  25.    1 IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  26.    1 IQQTFNLFSTKDSSAALDETLLDEFYIELDQQLNDLESCVMQEVGVIESPLMYEDSILAV
  27.    1 IQQTFNLFSTKDSSAALDETLLDEFYIELDQQLNDLEVLCDQEVGVIESPLMYEDSILAV
  28.    1 IQQTFNLFSTKDSSAAWDETLLDKFYIELFQQLNDLEACVTQEVGVEEIALMNEDSILAV
  29.    1 IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNEDFILAV
  30.    1 IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNNLEACVIQEVGMEETPLMNEDSILAV
  31.    1 IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNVDSILAV
  32.    1 IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNEDSILAV
  33.    1 IQQTFNLFSTKDSSATWEQSLLEKFSTELNQQLNDMEACVIQEVGVEETPLMNVDSILAV
  34.    1 MQQTFNLFSTKNSSAAWDETLLEKFYIELFQQMNDLEACVIQEVGVEETPLMNEDSILAV
  35.    1 IQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAV
  36.    1 IQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVMQEERVGETPLMNADSILAV
  37.    1 IQQTFNLFSTKDSSVAWDERLLDKLYTELYQQLNDLEACVMQEVWVGGTPLMNEDSILAV

   1.    1 KSYYWRVQRYLKLMKYNSYAWMVVRAEIFRNFLIIRRLTRNFQN
   2.    1 KKYYFNLVQYLESKEYNRCAWTVVRVQILTNFSFLMRLTASLRD
   3.    1 RKYYFNLVQYLKSKEYNRCAWTVVRVQILRNFSFLTRLTGYLRE
   4.    1 GKYYFNLMQYLESKEYDRCAWTVVQVQILTNVSFLMRLTGYVRD
   5.    1 KKYYGRISQYLKAKKYSHCAWTVVQAEMLRNLAFLNGLTDYLQN
   6.    1 KRYYGRILHYLKAKEYSHCAWTIVRVEILRNFYFINRLTGYLRN
   7.    1 KRYFQGIHVYLQEKGYSDCAWEIVRLEIMRSLSSSTSLQERLRM
   8.    1 KRYFRRIRLYLTEKKYSDCAWEIVRVDIMRSFSSSANLQGRLGM
   9.    1 KRYFRGIHLYLKEKKYSDCAWEIVRMEIMRSFSSSANLQGRLRM
  10.    1 RRYFQGIRVYLKEKKYSDCAWEVVRMEIMKSLFLSTNMQERLRS
  11.    1 REYFHRITVYLRENKHSPCAWEVVKAEVWRALSSSANLMGRLRE
  12.    1 RTYFHRITVYLRKKKHSLCAWEVIRAEVWRALSSSTNLLARLSE
  13.    1 RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSVNLLPRLSE
  14.    1 RTYFHRITVFLREKKHSPCAWEVVRAEVWRALSSSAKLLARLNE
  15.    1 RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSANVLGRLRE
  16.    1 RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSVNLLARLSK
  17.    1 RKYFHRLTLYLQEKRHSPCAWEVVRAEVMRAFSSSTNLQESFRR
  18.    1 RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQESFRR
  19.    1 RKYFHRLTLYLQEKRHSPCAWEVVRAEVMRAFSSSTNLQEKFRR
  20.    1 RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQERFRR
  21.    1 RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQERFRR
  22.    1 RRYFQRIALYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS---
  23.    1 RRYFQRIALYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS---
  24.    1 RRYFQRIALYLQEKKYSPCAWEIVRAEIMRCFSSSTNLQQS---
  25.    1 RRYFQRITLYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS---
  26.    1 RKYFQRITLYLTEKKYSSCAWEVVRAEIMRSFSLSINLQKRLKS
  27.    1 RKYFQRITLYLTEKKYSSCAWEVVRAEIMRSFSLSINLQKRLKS
  28.    1 RKYFQRITLYLMGKKYSPCAWEVVRAEIMRSFSFSTNLQKGLRR
  29.    1 RKYFQRITLYLMEKKYSPCAWEVVRAEIMRSFSFSTNLKKGLRR
  30.    1 RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSLSFSTNLQKILRR
  31.    1 RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSLSFSTNLQKRLRR
  32.    1 RKYFQRITLYLIERKYSPCAWEVVRAEIMRSLSFSTNLQKRLRR
  33.    1 KKYFQRITLYLTEKKYSPCAWEVVRAEIMRSFSLSKIFQERLRR
  34.    1 KKYFQRITLYLMEKKYSPCAWEVVRAEIMRSLSFSTNLQKRLRR
  35.    1 RKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRS
  36.    1 KKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLSTNLQERLRR
  37.    1 RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSFSSSRNLQERLRR

 Value profile:
     1      2      3      4      5      6      7      8      9     10
76.543 49.632 75.529 67.057 75.529 77.232 66.241 65.439 84.393 84.393

    11     12     13     14     15     16     17     18     19     20
89.610 84.393 84.393 85.220 91.499 83.581 84.393 93.473 88.246 88.246

    21     22     23     24     25     26     27     28     29     30
89.610 91.019 77.933 84.393 78.287 78.287 69.314 55.326 33.775 51.321

    31     32     33     34     35     36     37     38     39     40
52.484 40.683 86.923 85.639 74.213 87.360 88.246 74.213 68.454 85.639

    41     42     43     44     45     46     47     48     49     50
72.622 77.581 70.191 81.615 73.251 70.191 65.175 71.694 79.368 65.439

    51     52     53     54     55     56     57     58     59     60
88.246 84.804 75.529 75.864 89.610 79.005 81.615 83.985 80.477 81.615

    61     62     63     64     65     66     67     68     69     70
81.615 79.005 79.005 80.477 86.923 74.538 75.864 74.538 80.105 80.853

    71     72     73     74     75     76     77     78     79     80
80.477 78.287 70.488 77.581 41.898 41.898 77.933 74.538 76.202 79.005

    81     82     83     84     85     86     87     88     89     90
86.063 86.063 84.393 86.491 86.491 90.075 90.075 91.019 91.019 90.544

    91     92     93     94     95     96     97     98     99    100
86.491 83.181 84.393 86.063 83.581 83.581 88.246 80.105 82.784 86.491

   101    102    103    104    105    106    107    108    109    110
86.063 82.391 86.923 88.696 69.605 75.864 75.529 80.477 66.241 74.866

   111    112    113    114    115    116    117    118    119    120
73.569 79.368 76.886 84.393 84.393 84.393 83.581 83.181 79.368 77.933

   121    122    123    124    125    126    127    128    129    130
74.866 70.488 87.360 76.202 76.202 76.886 71.694 83.181 83.181 84.393

   131    132    133    134    135    136    137    138    139    140
82.001 80.105 77.581 76.886 51.321 63.119 59.048 52.879 69.897 65.704

   141    142    143    144    145    146    147    148    149    150
35.336 67.333 59.048 65.175 70.488 70.786 71.694 72.622 71.390 82.001

   151    152    153    154    155    156    157    158    159    160
83.581 88.246 87.801 88.246 88.696 91.019 94.495 94.495 96.075 95.015

   161    162    163    164
94.495 94.495 94.495 91.499
__________________________________________________________________



6. SEARCHING FOR PATTERNS IN COMBINATORIAL PEPTIDE LIBRARY.


1.  Go to the item  "File".
2.  Go to the item  "Protein".
3.  Select file "LIBRARY.ALI".
4.  Press "Alt I" to select all peptides and press "Esc".
5.  Go to the item "Options".
6.  Select "Sequence display mode" and switch to "sequence".
7.  Go to the item "Calculation".
8.  Select "Min frame". Press "Enter", type "3", press "Enter".
9.  Select "Max frame". Press "Enter", type "4", press "Enter".
10. Go to the item "Prep. data".
11. Move cursor to the first position and press "Alt B".
12. Move cursor to the last position and press "Alt E".
13. Press "F10" or "Esc" to go to the main menu.
14. Go to the item "Analysis".
15. Select "Motifs search".
16. Select matrix of amino acids similarity "ONE.MAT", press "ENTER", 
    type 25 as maximal % of acceptable mismatches.
17. Wait for calculation finishing.
18. Go to the item "Save last result", select the name of existing
    file or type new name if you want to save patterns to disk.
19. Go to the item "View last result" to see the table of patterns.
20. Select any pattern (the first, for example) and press "ENTER" to map 
    the pattern on the sequences. 
21. Go to the item "Prep. data" to view the pattern on the sequences.
    Selected pattern is marked in RED. 
22. To sort the sequences by presence of the pattern press "Alt S" and
    select item "SORT BY MOTIF". 
23. To change the font to display pattern press "F8". You'll get the
    following result: 

 Name               Act   Grp Line 1   Col 1

 CLONE 8819,58     1.000  1 lnDmSNhipspltlp
 CLONE 8893        1.000  1 lnDmSNhipspltlp
 CLONE 8833        1.000  1 lvDlSNsqsppalls
 CLONE 8875        1.000  1 lvDaSNmsnpvllla
 CLONE 8855,91     1.000  1 lvDvSNttmqlssvn
 CLONE 8884        1.000  1 lvDlSNrpvapnllg
 CLONE 8832        1.000  1 ltDlSNvtarnwtvs
 CLONE 8894        1.000  1 ltDkSNvphvwpypa
 CLONE 8861        1.000  1 ldDySNvprttqslp
 CLONE 8810,35     1.000  1 tiDmSNvyttptfps
 CLONE 8827,48     1.000  1 fdDwSNkspaslppt
 CLONE 8888        1.000  1 fvDlSNnvyssespn
 CLONE 8843        1.000  1 itDlSNmllpsppps
 CLONE 8845        1.000  1 itDlSNviapdtpky
 CLONE 8812        1.000  1 vnDmSNhipspltlp
 CLONE 8851,28,69  1.000  1 lqDnSNhlipsvppl
 CLONE 8841        1.000  1 fhthnmtDiSNrlps
 CLONE 8842        1.000  1 lsDqSNrpqftnlmr
 CLONE 8873        1.000  1 rvreedapnlslspi

24. The library can be further divided into subgroups with different
    patterns by changing group number for sequences with identified
    pattern (press "Cntl-Alt-2" to change the active group number to "2"
    and "Enter" to change the sequence group number) combined with sorting by
    group number. 

25. Press "F9" if you want to clear the pattern. 
 

26. Listing of the patterns saved to disk (see item #18):
_________________________________________________________________


Search motifs.
Number item   Length of peptide    Frequency    Sequence
1            4                   18           D-SN
2            4                    7           PD-P
3            4                    6           S-PP
4            4                    6           DLSN
5            4                    6           P-PP
6            4                    6           P-GQ
7            4                    6           GQ-P
8            3                    6           DLS
9            3                    6           LSN
10            3                    6           PDP
11            4                    5           VD-S
12            4                    5           TD-S
13            4                    5           P-PL
14            4                    5           SQ-P
15            4                    5           P-LL
16            4                    5           S-VP
17            3                    5           MSN
18            3                    5           SNV
19            3                    5           SLP
20            3                    5           QTP
21            4                    4           DMSN
22            4                    4           S-SP
23            4                    4           SE-P
24            4                    4           T-LS
25            4                    4           PS-P
__________________________________________________________________

Sequences with the main motif D-SN 


7. PROFILES OF PHYSICO-CHEMICAL PROPERTIES (EXAMPLE WITH HOPP-WOODS
HYDROPHILICITY).

1.  Go to the item "File".
2.  Go to the item "Property".
3.  Select file "Property.ppt".
4.  Press "Alt I" to select all properties and press "Esc".
5.  Go to the item "Protein".
6.  Select file "IFN.ALI".
7.  Press "Alt I" to select all proteins and press "Esc".
8.  Go to the item "Prep. data".
9.  Move cursor to the first position and press "Alt B".
10. Move cursor to the last position and press "Alt E".
11. Press "F10" or "Esc" to go to the main menu.
12. Go to the item "Options".
13. Go to the item "Calculation".
14. Select "Min frame". Press "Enter", type "7", press "Enter".
15. Select "Max frame". Press "Enter", type "7", press "Enter".
18. Go to the main menu (by pressing "Esc").
19. Go to the item "Analysis".
20. Select "Factors definition" and press "Enter".
21. Press "Enter" to select "Fragment 1 pos. 1-172.
22. Select "Average for a fragment" and press "Enter".
23. Switch property "Hydrophilicity Hopp-Woods" to "On" (by pressing "Enter")
24. Switch all other properties to "Off" (by pressing "Enter").
26. Return back to the menu item "Analysis" (by pressing "Esc").
27. Go to the item  "Profile analysis".
28. Select "Phys-chem profiles".
29. Select "Average profile".
21. Wait for calculation. After finishing the calculated profile
    will be shown.
22. Press "F2" if you want to print the profile.
23. Go to the item "Save profile", select the name of existing file or
    type new name if you want to save the profile to disk.
24. If protein 3D structure is loaded, you can map the profile on 3D
    structure:
25. Go to the item "View profile on    3D".
26. Type upper threshold for low values of the profile and press "ENTER".
27. Type low threshold for high values of the profile and press "ENTER".
28. You'll get stereo picture of protein in three colors that reflects
    the low, intermediate and high values of the profile (low values
    are in RED, intermediate values are in YELLOW and high values
    are in CYAN).
29. Sites with high profile values are possible surface regions.
30. Profile result:
_____________________________________________


 Average profile for fragment: 1-172
 Min-max frame: 7-7
 Function: Average for a fragment
 Property: Hydrophilicity Hopp-Woods

 Name sequence:
   1.   MO B pr.
   2.   BO B-3 pr.
   3.   BO B-2 pr.
   4.   BO B-1 pr.
   5.   HO B-I pr.
   6.   HU B-1 pr.
   7.   BO A-II-1 pr.
   8.   HO A-II-1 pr.
   9.   HO A-II-2 pr.
  10.   HU A-II-1 pr.
  11.   RA A-I-1 pr.
  12.   MO A-I-4 pr.
  13.   MO A-2 pr.
  14.   MO A-I-6 pr.
  15.   MO A-1 pr.
  16.   MO A-I-5 pr.
  17.   BO A-I-A pr.
  18.   BO A-I-C pr.
  19.   BO A-I-B pr.
  20.   BO A-I-D pr.
  21.   BO A-I-1 pr.
  22.   HO A-I-1 pr.
  23.   HO A-I-3 pr.
  24.   HO A-I-2 pr.
  25.   HO A-I-4 pr.
  26.   HU A-I-8 pr.
  27.   HU A-4 pr.
  28.   HU A-I-16 pr.
  29.   HU A-10 pr.
  30.   HU A-9 pr.
  31.   HU A-I-4B pr.
  32.   HU A-5 pr.
  33.   HU A-I-F pr.
  34.   HU A-I-14 pr.
  35.   HU A-2 pr.
  36.   HU A-1 pr.
  37.   HU A-I-6 pr.

 Aligned sequences:

   1. YKQLQLQERTNIRKCQELLEQLNGKI--NLTYRADFKIPMEMTEKMQ--KSYTAFAIQEM
   2. YSLLRFQQRRSAEVCQKLLGQLHSTPQHCLEAKMDFQVPEEMNQAQQFRKEDAILVIYEM
   3. YSLLRFQQRRSLALCQKLLRQLPSTPQHCLEARMDFQMPEEMKQAQQFQKEDAILVIYEM
   4. YSLLRFQQRQSLKECQKLLGQLPSTSQHCLEARMDFQMPEEMKQEQQFQKEDAILVMYEV
   5. YDLLRSQLRSSNSACLMLLRQLNGAPQRCPEDTMNFQVPEEIEQAQQFQKEDAALVIYEM
   6. YNLLGFLQRSSNFQCQKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQFQKEDAALTIYEM
   7. CDLSPNHVLVGRQNLRLLGQMRRLSPRFCLQDRKDFAFPQEMVEVSQFQEAQAISVLHEM
   8. CDLPASLDLRKQETLRVLHQMETISPPSCLKHRTDFRFPQEQLDGRQFPEAQATSVLQEM
   9. CDLPQNHILVSRKNFVLLGQMSRISSAICLKDRKDFRFPQDMADGRQFPEAQAASVLHEM
  10. CDLPQNHGLLSRNTLVLLHQMRRISPFLCLKDRRDFRFPQEMVKGSQLQKAHVMSVLHEM
  11. CDLPHTHNLRNKRVFTLLAQMRRLSPVSCLKDRKYFGFPLEKVDGQQIQKAQAIPVLHEL
  12. CDLPHTYNLGNKRALTVLEEMRRLPPLSCLKDRKDFGFPLEKVDNQQIQKAQAILVLRDL
  13. CDLPHTYNLRNKRALKVLAQMRRLPFLSCLKDRQDFGFPLEKVDNQQIQKAQAIPVLRDL
  14. CDLPQTHNLRNKRALTLLVKMRRLSPLSCLKDRKDFGFPQEKVGAQQIQEAQAIPVLTEL
  15. CDLPQTHNLRNKRALTLLVQMRRLSPLSCLKDRKDFGFPQEKVDAQQIKKAQAIPVLSEL
  16. CDLPQTHNLRNKRALTLLVKMRRLSPLSCLKDRKDFGFPQEKVGAQQIQEAQAIPVLSEL
  17. CHLPHTHSLANRRVLMLLQQLRRVSPSSCLQDRNDFEFLQEALGGSQLQKAQAISVLHEV
  18. CHLPHTHSLANRRVLMLLGQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  19. CHLPHTHSLPNRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  20. CHLPHSHSLAKRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  21. CHLPHSHSLAKRRVLTLLRQLRRVSPSSCLQDRNDFAFPQEALGGSQLQKAQAISVLHEV
  22. CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  23. CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  24. CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  25. CDLPHTHSLGNTRVLMLLGQMRRISPFSCLKDRNDFGFPQEVFDGNQFRKPQAISAVHET
  26. CDLPQTHSLGNRRALILLAQMRRISPFSCLKDRHDFEFPQEEFDDKQFQKAQAISVLHEM
  27. CDLPQTHSLGNRRALILLAQMRRISPFSCLKDRHDFEFPQEEFDDKQFQKAQAISVLHEM
  28. CDLPQTHSLGNRRALILLAQMGRISHFSCLKDRYDFGFPQEVFDGNQFQKAQAISAFHEM
  29. CDLPQTHSLRNRRALILLAQMGRISPFSCLKDRHEFRFPEEEFDGHQFQKTQAISVLHEM
  30. CDLPQTHSLGNRRALILLAQMGRISPFSCLKDRPDFGLPQEEFDGNQFQKTQAISVLHEM
  31. CDLPQTHSLGNRRALILLAQMGRISHFSCLKDRHDFGFPEEEFDGHQFQKTQAISVLHEM
  32. CDLPQTHSLGNRRALILLGQMGRISPFSCLKDRHDFRIPQEEFDGNQFQKAQAISVLHEM
  33. CDLPQTHSLGNRRALILLAQMGRISPFSCLKDRHDFGFPQEEFDGNQFQKAQAISVLHEM
  34. CNLSQTHSLNNRRTLMLMAQMRRISPFSCLKDRHDFEFPQEEFDGNQFQKAQAISVLHEM
  35. CDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEF-GNQFQKAETIPVLHEM
  36. CDLPETHSLDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEFDGNQFQKAPAISVLHEL
  37. CDLPQTHSLGHRRTMMLLAQMRRISLFSCLKDRHDFRFPQEEFDGNQFQKAEAISVLHEV

   1. LQNVFLVFRNNFSSTGWNETIVVRLLDELHQQTVFLKTVL-EEKQEERLTWEMSSTALHL
   2. LQQIFNILTRDFSSTGWSETIIEDLLVELYGQMNRLQPIQKEIMQEQNFTMGDTTV-LHL
   3. LQQIFNILTRDFSSTGWSETIIEDLLEELYEQMNHLEPIQKEIMQKQNSTMGDTTV-LHL
   4. LQHIFGILTRDFSSTGWSETIIEDLLKELYWQMNRLQPIQKEIMQKQNSTTEDTIV-PHL
   5. LQHTWRIFRRNFASTGWNETIVKNLLVEVHLQMDRLETNLEEIMEEESSTWGNTTI-LRL
   6. LQNIFAIFRQDSSSTGWNETIVENLLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHL
   7. LQQSFNLFHKERSSAAWDTTLLEQLLTGLHQQLDDLDACLGLLTGEEDSALGRTGPTLAM
   8. LQQIVSLFHTERSSAAWNTTLLDRLLAGLHQQLEDLNTCLDEQTGEEESALGTVGPTLAV
   9. LQQIFSLFHTERSSAAWNTTLLDELCTGLLRQLEDLDTCLEQEMGEEESALGTVRPTLAV
  10. LQQIFSLFHTERSSAAWNMTLLDQLHTELHQQLQHLETCLLQVVGEGESAGAISSPALTL
  11. TQQILSLFTSKESSTAWDATLLDSFCNDLQQQLSGLQACLMQQVGVQESPLTQEDSLLAV
  12. TQQILNLFTSKDLSATWNATLLDSFCNDLHQQLNDLKACVM-----QEPPLTQEDSLLAV
  13. TQQTLNLFTSKASSAAWNATLLDSFCNDLHQQLNDLQTCLMQQVGVQEPPLTQEDALLAV
  14. TQQILTLFTSKDSSAAWNATLLDSFCNDLHQLLNDLQGCLMQQVEIQALPLTQEDSLLAV
  15. TQQILNIFTSKDSSAAWNATLLDSFCNDLHQQLNDLQGCLMQQVGVQEFPLTQEDALLAV
  16. TQQVLNIFTSKDSSAAWNATLLDSFCNEVHQQLNDLKACVMQQVGVQESPLTQEDSLLAV
  17. TQHTFQLFSTEGSPATWDKSLLDKLRAALDQQLTDLQACLTQEEGLRGAPLLKEDSSLAV
  18. TQHTFQLFSTEGSATMWDESLLDKLRDALDQQLTDLQFCLRQEEELQGAPLLKEDSSLAV
  19. TQHTFQLFSTEGSATTWDESLLDKLHAALDQQLTDLQACLRQEEGLRGAPLLKEGSSLAV
  20. TQHTFQLSSTEGSAAVWDESLLDKLRTALDQQLTDLQACLRQEEGLPGAPLLKEDSSLAV
  21. TQHTFQLFSTEGSAAVWDESLLDRLRTALDQQLTDLQACLRQEEGLPGAPLLKEDSSLAV
  22. IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  23. IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  24. IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  25. IQQIFHLFSTDGSSAAWDESLLDKLYTGLYQQLTELEACLSQEVGVEETPLMNEDSLLAV
  26. IQQTFNLFSTKDSSAALDETLLDEFYIELDQQLNDLESCVMQEVGVIESPLMYEDSILAV
  27. IQQTFNLFSTKDSSAALDETLLDEFYIELDQQLNDLEVLCDQEVGVIESPLMYEDSILAV
  28. IQQTFNLFSTKDSSAAWDETLLDKFYIELFQQLNDLEACVTQEVGVEEIALMNEDSILAV
  29. IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNEDFILAV
  30. IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNNLEACVIQEVGMEETPLMNEDSILAV
  31. IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNVDSILAV
  32. IQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNEDSILAV
  33. IQQTFNLFSTKDSSATWEQSLLEKFSTELNQQLNDMEACVIQEVGVEETPLMNVDSILAV
  34. MQQTFNLFSTKNSSAAWDETLLEKFYIELFQQMNDLEACVIQEVGVEETPLMNEDSILAV
  35. IQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAV
  36. IQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVMQEERVGETPLMNADSILAV
  37. IQQTFNLFSTKDSSVAWDERLLDKLYTELYQQLNDLEACVMQEVWVGGTPLMNEDSILAV

   1. KSYYWRVQRYLKLMKYNSYAWMVVRAEIFRNFLIIRRLTRNFQN--------
   2. KKYYFNLVQYLESKEYNRCAWTVVRVQILTNFSFLMRLTASLRD--------
   3. RKYYFNLVQYLKSKEYNRCAWTVVRVQILRNFSFLTRLTGYLRE--------
   4. GKYYFNLMQYLESKEYDRCAWTVVQVQILTNVSFLMRLTGYVRD--------
   5. KKYYGRISQYLKAKKYSHCAWTVVQAEMLRNLAFLNGLTDYLQN--------
   6. KRYYGRILHYLKAKEYSHCAWTIVRVEILRNFYFINRLTGYLRN--------
   7. KRYFQGIHVYLQEKGYSDCAWEIVRLEIMRSLSSSTSLQERLRMMDGDLKSP
   8. KRYFRRIRLYLTEKKYSDCAWEIVRVDIMRSFSSSANLQGRLGMKDGDLGSP
   9. KRYFRGIHLYLKEKKYSDCAWEIVRMEIMRSFSSSANLQGRLRMKDGDLGSP
  10. RRYFQGIRVYLKEKKYSDCAWEVVRMEIMKSLFLSTNMQERLRSKDRDLGSS
  11. REYFHRITVYLRENKHSPCAWEVVKAEVWRALSSSANLMGRLREERNES---
  12. RTYFHRITVYLRKKKHSLCAWEVIRAEVWRALSSSTNLLARLSEEKE-----
  13. RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSVNLLPRLSEEKE-----
  14. RTYFHRITVFLREKKHSPCAWEVVRAEVWRALSSSAKLLARLNEDE------
  15. RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSANVLGRLREEK------
  16. RKYFHRITVYLREKKHSPCAWEVVRAEVWRALSSSVNLLARLSKEE------
  17. RKYFHRLTLYLQEKRHSPCAWEVVRAEVMRAFSSSTNLQESFRRKD------
  18. RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQESFRRKD------
  19. RKYFHRLTLYLQEKRHSPCAWEVVRAEVMRAFSSSTNLQEKFRRKD------
  20. RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQERFRRKD------
  21. RKYFHRLTLYLQEKRHSPCAWEVVRAQVMRAFSSSTNLQERFRRKD------
  22. RRYFQRIALYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS-----------
  23. RRYFQRIALYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS-----------
  24. RRYFQRIALYLQEKKYSPCAWEIVRAEIMRCFSSSTNLQQS-----------
  25. RRYFQRITLYLQEKKYSPCAWEIVRAEIMRSFSSSTNLPQS-----------
  26. RKYFQRITLYLTEKKYSSCAWEVVRAEIMRSFSLSINLQKRLKSKE------
  27. RKYFQRITLYLTEKKYSSCAWEVVRAEIMRSFSLSINLQKRLKSKE------
  28. RKYFQRITLYLMGKKYSPCAWEVVRAEIMRSFSFSTNLQKGLRRKD------
  29. RKYFQRITLYLMEKKYSPCAWEVVRAEIMRSFSFSTNLKKGLRRKD------
  30. RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSLSFSTNLQKILRRKD------
  31. RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSLSFSTNLQKRLRRKD------
  32. RKYFQRITLYLIERKYSPCAWEVVRAEIMRSLSFSTNLQKRLRRKD------
  33. KKYFQRITLYLTEKKYSPCAWEVVRAEIMRSFSLSKIFQERLRRKE------
  34. KKYFQRITLYLMEKKYSPCAWEVVRAEIMRSLSFSTNLQKRLRRKD------
  35. RKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE------
  36. KKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLSTNLQERLRRKE------
  37. RKYFQRITLYLTEKKYSPCAWEVVRAEIMRSFSSSRNLQERLRRKE------

 Value profile:
     1      2      3      4      5      6      7      8      9     10
-0.267 -0.058 -0.512 -0.171 -0.071  0.158  0.597  0.597  0.319  0.367

    11     12     13     14     15     16     17     18     19     20
 0.116 -0.200 -0.515 -0.799 -0.878 -0.409  0.036 -0.012  0.294  0.296

    21     22     23     24     25     26     27     28     29     30
 0.054  0.220 -0.142 -0.742 -0.202  0.093  0.555  0.763  1.145  0.926

    31     32     33     34     35     36     37     38     39     40
 1.309  0.646  0.285 -0.056  0.329  0.053  0.211  0.361  0.716  0.786

    41     42     43     44     45     46     47     48     49     50
 0.740 -0.006 -0.021  0.615  0.336  0.396  0.259 -0.000  0.290  0.013

    51     52     53     54     55     56     57     58     59     60
-0.669 -0.744 -0.407 -0.523 -0.489 -0.437 -0.240 -0.142 -0.415 -0.827

    61     62     63     64     65     66     67     68     69     70
-0.892 -1.035 -1.029 -1.009 -0.447  0.077  0.092  0.377  0.644  0.540

    71     72     73     74     75     76     77     78     79     80
 0.037 -0.092 -0.037 -0.062 -0.349 -0.531 -0.050  0.746  0.164 -0.200

    81     82     83     84     85     86     87     88     89     90
-0.229  0.297  0.297 -0.210 -0.508 -0.184 -0.299 -0.232 -0.157 -0.158

    91     92     93     94     95     96     97     98     99    100
 0.237  0.144 -0.031 -0.005 -0.013 -0.260  0.228 -0.157 -0.048  0.061

   101    102    103    104    105    106    107    108    109    110
 0.509  0.803  0.627  0.370  0.204  0.051  0.202  0.230  0.225  0.282

   111    112    113    114    115    116    117    118    119    120
 0.143  0.128  0.173 -0.169  0.014  0.117 -0.203 -0.402 -0.167  0.252

   121    122    123    124    125    126    127    128    129    130
 0.218 -0.244 -0.830 -0.831 -0.735 -0.573 -0.594  0.063  0.525  0.467

   131    132    133    134    135    136    137    138    139    140
 0.848  1.179  0.884  0.473 -0.414 -0.485 -0.456 -0.724 -0.391 -0.345

   141    142    143    144    145    146    147    148    149    150
 0.090  0.334 -0.261  0.364  0.581 -0.141 -0.028 -0.525 -0.288 -0.081

   151    152    153    154    155    156    157    158    159    160
-0.398 -0.656 -0.362 -0.134  0.210 -0.033  0.313  0.478  1.060  1.410

   161    162    163    164    165    166    167    168    169    170
 1.357  1.548  2.407  2.389  2.683  2.633  0.000  0.000  0.000  0.000

   171    172
 0.000  0.000
__________________________________________________________________




