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TUTORIAL.TXT
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1992-08-13
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TUTORIAL
LESSON 1. Basic Functions
1) Using the Convert Program
2) Loading a Gel
3) Compare Lanes Directly
4) Compare Lanes Using Standards
This lesson is designed to teach the use of the Convert program and
the basic functions of DNA SIMDEX. We will be practicing using a
simple file that contains four DNA lanes.
__________________________________________________________________
| | | | | Origin Lane 1
| ||| | Origin Lane 2
| | | | | Origin Lane 3
| ||| | Origin Lane 4
------------------------------------------------------------------
The (X,Y) coordinates of these bands and lane origins are shown
below.
20,10 -------
40,10 | Lane 1
60,10 |
400,10 -------
26,20 -------
32,20 | Lane 2
38,20 |
400,20 -------
10,30 -------
20,30 | Lane 3
30,30 |
200,30 -------
13,40 -------
16,40 | Lane 4
19,40 |
200,40 -------
We have created an (X,Y) coordinate file for these lanes in a word
processing program. This (X,Y) coordinate file is on the DNA
SIMDEX disk under the name "Demo1.doc". To view the file, select
the appropriate drive at the DOS prompt and type "Type Demo1.doc"
<Enter>. DOS will display the (X,Y) coordinate file on your
monitor.
In order to use (X,Y) coordinate files on DNA SIMDEX, we must first
convert them to DNA SIMDEX files. A program called "CONVERT" has
been written to make this conversion as simple as possible. Follow
the steps outline below to convert "Demo1.doc" to a DNA SIMDEX
file.
1) Select the appropriate drive. If, for example, the DNA SIMDEX
disk is in drive "A" type "A:" <ENTER> to change to drive "A".
2) Type "CONVERT" <Enter>. CONVERT's main menu should be displayed
on your monitor.
---------CONVERT Main Menu------------
| |
| 1) File to File Conversion |
| 2) Hand Entry to File Conversion |
| 3) Quit |
|______________________________________|
3) Select File to File Conversion by pressing "1". The program
will change screens and prompt you for the name of the file to be
converted.
----File to File Conversion Screen----
| |
| File Name for Conversion:? _______ |
| |
|______________________________________|
4) Type "Demo1.doc" <Enter>. This tells the program that Demo1.doc
is the (X,Y) coordinate file you would like to be converted.
5) The program will prompt you for the total number of bands and
lane origins in "Demo1.doc". "Demo1.doc" has four lanes, each of
which have 3 bands and 1 lane origin. Totaling them up,
"Demo1.doc" has 16 bands and lane origins. Type "16" <Enter>.
-----File to File Conversion Screen-----------
| |
| File Name for Conversion:? Demo1.doc |
| Total Number of Bands & Lane Origins:? 16 |
|______________________________________________|
6) The program will prompt you for a new file name. This will be
the name of the DNA SIMDEX file created by CONVERT. Let's call the
new file, "Demo1". Type "Demo1" <Enter>.
-------File to File Conversion Screen---------
| |
| File Name for Conversion:? Demo1.doc |
| Total Number of Bands & Lane Origins:? 16 |
| New File Name:? Demo1 |
| Conversion Complete. <Press Enter> |
|______________________________________________|
You have just converted an (X,Y) coordinate file to a DNA SIMDEX
file!
7) Press <ENTER> to return to the main menu.
8) Press "3" to exit the CONVERT program.
If you type "DIR" <ENTER> you will see a listing of the files now
present on the DNA SIMDEX disk. "Demo1" should be one of the files
listed.
Now that you have created a DNA SIMDEX file, you can analyze the
DNA lanes on DNA SIMDEX. To analyze the data follow the steps
below.
1) With the proper drive selected, type "SIMDEX" <Enter>. The
title screen for DNA SIMDEX 2.0 will be displayed.
2) Press any key to advance to the main menu.
-------DNA SIMDEX Main Menu-----------
| |
| 1) Load a Gel |
| 2) Compare Lanes Directly |
| 3) Compare Lanes Using Standards |
| 4) Manipulate Values |
| 5) Band Flagging Setup |
| 6) Quit |
| 7) Parameter Set |
| 8) Gel Setup |
| 9) Designate Output File |
|______________________________________|
3) Before making any comparisons, we must load the DNA SIMDEX file
we have previously created. Press "1" to Load a Gel.
--Load a Gel Screen--
| |
| FILE NAME:? |
|_____________________|
4) The program will prompt you for a filename to be loaded.
Respond by typing "Demo1" <Enter>. This tells the program to load
the DNA SIMDEX file we created with the CONVERT program.
5) The program will prompt you for a Gel I.D. This I.D. can be a
name, number, or code that will be used to identify the DNA gel
from this file throughout the remainder of the session. (Since
most files contain the information from one electrophoretic gel or
autoradiogram, we often use the words gel and file
interchangeably.) To keep things simple lets make the Gel I.D.
"Demo1". Type "Demo1" <Enter>.
--------Load a Gel Screen---------
| |
| FILE NAME:? Demo1 |
| GEL I.D. ? Demo1 |
| LOADING LANE 4 |
| THIS GEL HAS A TOTAL OF 4 LANES |
| <Strike Any Key> |
|__________________________________|
The program will open the DNA SIMDEX FILE "DEMO1" and enter the
coordinates into memory. The program also assigns each lane a
number. In this case, the lanes will be numbered from 1 to 4.
These are computer-assigned lane numbers. If we had already loaded
a file, the computer would assign each lane a number starting with
the last lane number assigned to the previous file. The program
also assigns an in-gel lane number to each lane according to its
position in the gel. The first lane in a gel will have an in-gel
number of 1. The second lane in a gel will have an in-gel number
of 2 and so on. This is true even if other gels have been loaded
previously. For example, if Gel #1 was loaded before Gel #2, the
lanes would be assigned the following numbers.
GEL # Computer-Assigned In-Gel
Lane Numbers Lane Numbers
1 1 1
1 2 2
1 3 3
1 4 4
2 5 1
2 6 2
2 7 3
2 8 4
These numbers are use to designate lanes for comparison.
6) Now that you have loaded the information from "Demo1" you can
return to the main menu by pressing any key.
-------DNA SIMDEX Main Menu-----------
| |
| 1) Load a Gel |
| 2) Compare Lanes Directly |
| 3) Compare Lanes Using Standards |
| 4) Manipulate Values |
| 5) Band Flagging Setup |
| 6) Quit |
| 7) Parameter Set |
| 8) Gel Setup |
| 9) Designate Output File |
|______________________________________|
The next step is to compare the DNA lanes in "Demo1". Follow the
steps outline below to compare lanes 1 and 2 of "Demo1".
1) Select Compare Lanes Directly by pressing "2".
2) The program will prompt you for a method of selecting the lanes
for comparison. Lanes can be selected according to the computer-
assigned lane numbers or by entering the Gel I.D. and the in-gel
lane number.
Let's use the computer-assigned lane numbers. Press "1".
--------Lane Selection Window--------
| |
| Lane Selection By.... |
| 1) Lane Number |
| 2) Gel I.D. and In-Gel Lane Number |
|_____________________________________|
3) The program will prompt you for two lane numbers. We want to
compare lanes 1 and 2 so type "1" <ENTER> and then "2" <Enter>.
This tells the program to compare the two lanes.
--Lane Designation Screen--
| |
| First Lane 1 |
| Second Lane 2 |
|___________________________|
4) The program will make the comparison and the Results Screen will
be displayed on your monitor.
_________________________________________________________________
| Similarity Index = .666666666666 |
| _______________________________________________________________ |
| Demo1, Lane 1 Demo1, Lane 2 |
| Matching Bands = 2 Matching Bands = 2 |
| |
| 1 (1) 2(3) 1 (1) 3 (2) |
| |
| Non-Matching Bands = 1 Non-Matching Bands = 1 |
| |
| 3 2 |
| |
-----------------------------------------------------------------
| (1) Return to Main Menu (2) Print (3) Save (4) Match Edit |
| (5) Perform Another Comp. (6) Up (7) Down (8) Notes (9) Map |
-----------------------------------------------------------------
The Results Screen tells us that band 1 of lane #1 matches with
band 1 of lane #2. (The numbers in parenthesis correspond to the
matching band in the other lane.) Also, band 2 of lane #1 matches
with band 3 of lane #2. The similarity index for this comparison
is 0.6666.
There are several options that can be accessed from the results
screen. Lets try a few of them.
First, lets look at a map of the comparison we just made. Press
"9" for a high resolution map. The screen should have changed to
show the location of the bands in lanes 1 and 2. The first lane in
the comparison is always shown above the second lane. Matching
bands are shown in pink while non-matching bands are shown in
white. Press any key to return to the Results Screen.
If you have a printer connected to your computer, print out the
results. Press "2" for a printout.
You can also save the results of a comparison. Press "3" to save
the results.
-----Saving Results Screen-----
| |
| File Name:? _________ |
|_______________________________|
Let's save the results as "Results" Type "Results" <Enter>. You
have just save the results in a file entitled, "RESULTS".
In addition to saving the results we can also attach notes to a
file. Press "8" to create explanatory notes.
------------------------Notes Screen----------------------------
| |
| Notes Demo1, Lane 1 and Demo1, Lane 2 |
| Line 1: |
|________________________________________________________________|
The program will allow you up to 10 lines of text. Go ahead and
write anything pressing <ENTER> after each line.
-----------------------Notes Screen----------------------------
| |
| Notes form Demo1, Lane 1 and Demo1, Lane 2 |
| Line 1___Bla bla bla________________________________________ |
| Line 2___I like to write notes______________________________ |
| Line 3___Bla Bla____________________________________________ |
| Line 4___My name is_________________________________________ |
| Line 5___my dog has_________________________________________ |
| Line 6___bigger fleas_______________________________________ |
| Line 7___than_______________________________________________ |
| Line 8___your_______________________________________________ |
| Line 9___dog________________________________________________ |
| Line 10__has________________________________________________ |
| (1) Save Notes (2) Retype Notes (3) Exit |
|_______________________________________________________________|
When you have completed the 10 lines instruct the program to save
the note by pressing "1". Let's put the note at the end of the
results. You can do this by typing "RESULTS" <ENTER> when prompted
for a file name. Your notes have been added to the end of the
"RESULTS" file.
If we disagree with the program's matching of bands, we can edit
the results by selecting "4" Match Edit. Let's say that we do not
agree with the matching of the first bands in both lanes. Press
"4" to Match Edit.
--Match Edit Screen--
| |
| (1) Match |
| (2) Unmatch |
|_____________________|
Select the unmatching function by pressing "2". Now type "1"
<ENTER> to indicate that band number 1 in the first lane has been
mismatched. The program returns to the Results Screen and you can
see that band 1 has been unmatched. Use the "9" key to see a map
of the new results.
To rematch the bands press "4" to Match Edit. Select the matching
function by pressing "1". Indicate that you want to match band 1
by typing "1" <Enter>. Indicate that you want to match band 1 in
lane 1 to band 1 in lane 2 by typing another "1" <Enter>. The
first bands in both lanes are now matched. Use the "9" key to see
view the results.
The "6" and "7" keys control the scrolling of the windows in the
Results Screen. The DNA samples we are comparing are relatively
simple and all of the data can be shown at once. If all of the
bands are not shown on the screen, the "6" and "7" keys can be used
to scroll the windows to show all of the bands.
Now that we have explored the Results Screen lets make another
comparison. Press "5" to Perform Another Comparison.
Once again the program prompts asks you how you would like to
select lanes.
-------Lane Selection Window---------
| |
| Lane Selection By |
| 1) Lane Number |
| 2) Gel I.D. and In-Gel Lane Number |
|_____________________________________|
This time, let's compare lanes 3 and 4 using the Gel I.D. and In-
gel Lane option. Press "2" to select the Gel I.D. and In-gel Lane
option.
The program will ask for the Gel I.D. Remember that we called this
gel "Demo1". Type "Demo1" <Enter>. Be sure that all of the
letters are in the same case as you originally typed the I.D. DNA
SIMDEX is case sensitive and will not recognize "DEMO1" the same as
"Demo1".
--Lane Designation Screen--
| |
| Gel I.D. Demo1 |
| Lane Number _____ |
|___________________________|
Now type "3" <ENTER> indicating that you want lane 3 to be the
first lane of the comparison.
The program will prompt you for the Gel I.D. of the second lane.
Once again type "Demo1" <Enter>.
--Lane Designation Screen--
| |
| Gel I.D. Demo1 |
| Lane Number 3 |
| Gel I.D. Demo1 |
| Lane Number _____ |
|___________________________|
Now type "4" <ENTER> indicating that you want lane 4 to be the
second lane of the Comparison.
The program will make the comparison and the Results Screen will be
displayed. Go ahead and try some of the Results Screen functions.
When you are finished, press "1" to return to the main menu.
Sometimes we want to compare lanes between gels. However, two gels
are rarely identical. The Compare Lanes Using Standards option
allows us to stretch or shrink lanes by using reference lanes as
standards.
Let's says that lanes 1 and 2 in "Demo1" are from one gel and that
lanes 3 and 4 are from a different gel. The DNA samples used for
lanes 1 and 3, and 2 and 4 are the same, but the gels were run
under different conditions. We want to compare lanes 2 and 4 using
lanes 1 and 3 as references.
__________________________________________________________________
| | | | | Origin Lane 1
| ||| | Origin Lane 2
| | | | | Origin Lane 3
| ||| | Origin Lane 4
------------------------------------------------------------------
To compare lanes 2 and 4 using standards, follow the steps
described below.
1) From the main menu, press "3" Compare Lanes Using Standards.
-------DNA SIMDEX Main Menu-----------
| |
| 1) Load a Gel |
| 2) Compare Lanes Directly |
| 3) Compare Lanes Using Standards |
| 4) Manipulate Values |
| 5) Band Flagging Setup |
| 6) Quit |
| 7) Parameter Set |
| 8) Gel Setup |
| 9) Designate Output File |
|______________________________________|
2) The program will ask you how you would like to identify the
lanes.
-------Lane Selection Window----------
| |
| Lane Selection By.... |
| 1) Lane Number |
| 2) Gel I.D. and In-Gel Lane Number |
|______________________________________|
Lets use the computer-assigned lane numbers. Press "1".
3) The program will prompt you for the first reference lane.
--Lane Designation Screen--
| |
| First Standard Lane_____ |
|___________________________|
Type "1" <ENTER> indicating that lane 1 is your first reference.
4) The program will prompt you for the second reference lane. Type
"3" <ENTER> indicating that lane 3 is your second reference lane.
--Lane Designation Screen--
| |
| First Standard Lane: 1 |
| Second Standard Lane: 3 |
|___________________________|
5) The program will prompt you for the first Known/Unknown lane.
This is the lane that is to be used for comparison. Type "2"
<Enter>.
-----Lane Designation Screen-----
| |
| First Standard Lane: 1 |
| Second Standard Lane: 3 |
| First Known/Unknown Lane: 2 |
| Second Known/Unknown Lane:_____ |
|__________________________________|
6) The program will prompt you for the second Known/Unknown lane.
This is the second lane for comparison. Type "4" <Enter>.
The program will take ratios between the bands in lanes 1 and 3 and
then use these ratios to stretch lane 4 for comparison with lane 2.
When the process is complete, the program will display the Results
Screen.
_________________________________________________________________
| Similarity Index 1 |
|_________________________________________________________________|
| Demo1, Lane 1 Demo1, Lane 2 |
| Matching Bands = 3 Matching Bands = 3 |
| |
| 1 (1) 2(2) 1 (1) 2 (2) |
| 3 (3) 3 (3) |
| |
| Non-Matching Bands = 0 Non-Matching Bands = 0 |
| |
| |
| |
-----------------------------------------------------------------
| (1) Return to Main Menu (2) Print (3) Save (4) Match Edit |
| (5) Perform Another Comp. (6) Up (7) Down (8) Notes (9) Map |
-----------------------------------------------------------------
The high resolution map of the results screen (9) will display the
first lane of the comparison (lane 2) in its normal position. The
second lane (lane 4) will be displayed in its stretched form.
All other functions of the Results Screen will function as they did
for a direct comparison.
To terminate this session, return to the Main Menu (1) and press
"6" to quit.
You have saved the results of at least one comparison as well as an
explanatory note in a file called "Results". This file can be
loaded into a word processing program. The file will contain extra
commas and quotation marks that can be deleted using the word
processor's search and replace function.
TUTORIAL
LESSON 2: Advanced functions
1) Manual Entry Using the Convert Program
2) Gel Setup
3) Designate Output File
4) Manipulating Data
This lesson is designed to teach some of the advanced functions of
the CONVERT and DNA SIMDEX programs. We will be practicing with
the sample gel shown below.
__________________________________________________________
10 | | | | | | | Origin Lane 1
20 | | | | | | | Origin Lane 2
30 |__________________________________________________________
30 54 58 62 74 260
34 56 60 64 110 259
The (X,Y) coordinates of each band and lane origin have been
measured from the top left hand corner of the gel. Y coordinates
are shown on the left of the gel while X coordinates are shown on
the bottom. Once these coordinates have been measured we can group
the coordinates into lanes.
30,10 -----
54,10 | Lane 1
58,10 |
62,10 |
74,10 |
260,10 -----
34,20 -----
56,20 | Lane 2
60,20 |
64,20 |
110,20 |
259,20 -----
DNA SIMDEX has a built-in function that will separate bands and
lane origins into separate lanes. If a coordinate has a Y value
that is within 5 pixels of the Y value of the coordinate before it,
the two will be grouped in the same lane. For example, bands with
a centers of gravity at (30,14) and (40,19) would be in the same
lane (Y values differ by 5) but bands with centers of gravity at
(30,14) and (40,20) would be assigned to different lanes (Y values
differ by 6). The coordinates that we have just plotted have a
difference of 10 in their Y values insuring that DNA SIMDEX will
recognize that there are two different lanes in this gel.
Now that we have the coordinates organized, we can use the CONVERT
program to make a DNA SIMDEX file. Follow the steps outlined below
to make a DNA SIMDEX file.
1) Place the DNA SIMDEX disk in the appropriate drive.
2) Type "CONVERT" <ENTER>. CONVERT's main menu should appear on
your monitor.
----------CONVERT Main Menu---------
| |
| (1) File to File Conversion |
| (2) Hand Entry to File Conversion |
| (3) Quit |
|____________________________________|
3) This time we want to enter the coordinates by hand. Press "2"
for Hand Entry to File Conversion.
-----------Hand To File Conversion Screen-----
| |
| New File Name:? |
|______________________________________________|
4) The program needs to know the title we want for our DNA SIMDEX
file. Let's call it "DEMO2". Type "DEMO2" <ENTER>.
-----------Hand To File Conversion Screen-----
| |
| New File Name:? DEMO2 |
| Total Number of Bands & Lane Origins:? |
|______________________________________________|
5) We need to tell the program how many bands and lane origins we
will be entering into the DNA SIMDEX file. Each of the two lanes
has 5 bands and 1 lane origin for a total of 12 bands and lane
origins. Type "12" <ENTER>.
-----------Hand To File Conversion Screen-----
| |
| New File Name:? DEMO2 |
| Total Number of Bands & Lane Origins:? 12 |
| X coordinate for #1 ? |
|______________________________________________|
6) The program will ask for the (X,Y) coordinates of each of the 12
bands and lane origins. Referring to the list below, enter each of
the coordinates.
30,10
54,10
58,10
62,10
74,10
260,10
34,20
56,20
60,20
64,20
110,20
259,20
When you have entered all of the coordinates the screen should look
like this.
-----------Hand To File Conversion Screen-----
| |
| New File Name:? DEMO2 |
| Total Number of Bands & Lane Origins:? 12 |
| X coordinate for #12 259 |
| Y coordinate for #12 20 |
| File Complete <ENTER> |
|______________________________________________|
You have just created a DNA SIMDEX file!
7) Press <ENTER> to return to the main menu.
----------CONVERT Main Menu---------
| |
| (1) File to File Conversion |
| (2) Hand Entry to File Conversion |
| (3) Quit |
|____________________________________|
8) Press "3" to exit to the system.
After we have created a DNA SIMDEX file we can begin using DNA
SIMDEX to analyze the data. Follow the steps outlined below to
begin your DNA SIMDEX session.
1) Type "SIMDEX" <ENTER>. The Title Screen should appear. Press
any key to continue to the main menu.
-------DNA SIMDEX Main Menu-----------
| |
| 1) Load a Gel |
| 2) Compare Lanes Directly |
| 3) Compare Lanes Using Standards |
| 4) Manipulate Values |
| 5) Band Flagging Setup |
| 6) Quit |
| 7) Parameter Set |
| 8) Gel Setup |
| 9) Designate Output File |
|______________________________________|
2) Press "1" to Load a Gel. The Load a Gel Screen will be
displayed on your monitor.
--Load a Gel Screen--
| |
| FILE NAME:? |
|_____________________|
3) Load "DEMO2" by typing "DEMO2" <ENTER>
4) Let's make the Gel I.D. "DEMO2" as well. Type "DEMO2" <ENTER>.
5) Strike any key to return to the main menu.
-------DNA SIMDEX Main Menu-----------
| |
| 1) Load a Gel |
| 2) Compare Lanes Directly |
| 3) Compare Lanes Using Standards |
| 4) Manipulate Values |
| 5) Band Flagging Setup |
| 6) Quit |
| 7) Parameter Set |
| 8) Gel Setup |
| 9) Designate Output File |
|______________________________________|
Now that we have loaded the gel into the computer, we can also give
names to each lane. This is done through the gel setup function.
Follow the steps outlined below to name lanes 1 and 2.
1) Press "8" from the main menu. The Gel Setup Screen will appear
on you monitor.
----------Gel Setup Screen-----------
| Enter Number of first a lane:? |
|_____________________________________|
2) The program will prompt you for a beginning and ending lane
number. This tells the program which lanes we want to name. Press
"1" <ENTER> to tell the program that we want to start naming from
lane 1.
----------Gel Setup Screen-----------
| Enter Number of First a Lane:? 1 |
| Enter Number of Last Lane:? |
|_____________________________________|
3) Press "2" <ENTER> to instruct the program that we want to stop
after naming lane 2.
4) The program will prompt you for the names of the two lanes.
Let's name the first lane "Sample 1". Type "Sample 1" <ENTER>.
Let's name the second lane "Sample 2". Type "Sample 2" <ENTER>.
The names that we have given these lanes will be used in the
Results Screen and in any printed or saved material created in this
session.
Now that we have named the two lanes, lets designate an output file
for use through the session. By designating a filename, we
instruct the program to save results and explanatory notes in a
single location throughout the session. To designate an output
file, follow the steps outlined below.
1) From the main menu, press "9" to designate an output file. The
designate output screen will appear on your monitor.
---------Designate Output Screen----------
| |
| Enter Name of Designated File:? |
|__________________________________________|
2) Tell the program to designate "OUTPUT" as our output file for
this session. Type "OUTPUT" <ENTER>. If we had just pressed
<ENTER> no output file would have been declared and the program
would prompt us for a file name each time we went into a save
function.
----------------Designate Output Screen----------------
| |
| Enter Name of Designated File:? OUTPUT |
| Do You want Matching Bands Printed and Saved (Y/N) |
|_______________________________________________________|
3) The program will prompt you if you want to include a list of
Matching bands in your files and print outs. Type "N" for no or
"Y" for yes.
4) The program will prompt you if you want to include a list of
non-matching bands in your files and print outs. Type "n" for no
or "y" for yes.
Instead of prompting us for an output file name, the program will
automatically use the "OUTPUT" file. You can test the functions we
have discussed by performing direct comparison between lanes 1 and
2
1) From the main menu, press "2" to compare lanes directly.
2) Press "1" to select lanes by computer-assigned lane numbers.
3) Type "1" <ENTER> to indicate that lane one is to be the first
lane of the comparison.
4) Type "2" <ENTER> to indicate that lane two is to be the second
lane of the comparison.
The Results Screen should be displayed on your monitor.
_________________________________________________________________
| Similarity Index = .600 |
| _______________________________________________________________ |
| DEMO2, Sample 2 DEMO2, Sample 2 |
| Matching Bands = 2 Matching Bands = 2 |
| |
| 3 (2) 4(3) 2 (3) 3 (4) |
| |
| Non-Matching Bands = 3 Non-Matching Bands = 3 |
| |
| 1 2 1 4 |
| 5 5 |
-----------------------------------------------------------------
| (1) Return to Main Menu (2) Print (3) Save (4) Match Edit |
| (5) Perform Another Comp. (6) Up (7) Down (8) Notes (9) Map |
-----------------------------------------------------------------
Notice, the lanes are now identified according to the names we have
given them. To save the results of this comparison, press "3".
The program will not prompt you for an output file name. Instead,
the results are automatically save to "OUTPUT". The same is true
when we save explanatory notes.
Lets look at the high resolution map of the comparison by pressing
"9". Although the program has matched some bands, it appears that
the lanes need to be shifted to alien. This is often the case with
lanes that are close to the edge in an autoradiogram. Perhaps the
best thing to do is to shift lane 1 to the right by a constant
value.
To shift the bands in lane 1, exit to the main menu by pressing "1"
from the Results Screen and follow the steps outlined below.
1) Press "4" to Manipulate Values. The Manipulate Values screen
will be displayed on your monitor.
---------Manipulate Values-----
| 1) Shift Values |
| 2) Delete Values |
| 3) View Lanes |
| 4) Main Menu |
|_______________________________|
2) From this menu we can shift bands to the right or left, delete
bands, and view lanes. Press "1" to shift values.
-----------------Shift Values--------------
| |
| Lane Selection By... |
| (1) Lane Number |
| (2) Gel I.D. and In-Gel Lane Number |
|___________________________________________|
3) Press "1" to select lanes by computer-assigned lane numbers.
-----------------Shift Values--------------
| |
| Lane Selection By... |
| (1) Lane Number |
| (2) Gel I.D. and In-Gel Lane Number |
| Enter Lane Number:? |
|___________________________________________|
4) Type "1" <ENTER> to shift the bands in lane "1".
5) Let's shift the bands to the right by 2 pixels. Type "2"
<ENTER>. A check window will be displayed.
------------Check Window----------
| |
| (A) Accept Shift |
| (X) Escape and No Change |
| (M) See Map of change (OLD/NEW) |
|__________________________________|
6) The program will prompt you to either accept or reject the
changes. If you wish, you can see a map of the changes by pressing
"M". We want to accept the change. Press "A". The manipulate
values screen will appear on your monitor.
---------Manipulate Values-----
| 1) Shift Values |
| 2) Delete Values |
| 3) View Lanes |
| 4) Main Menu |
|_______________________________|
7) Return to the main menu by pressing "4"
Now that we have shifted lane 1, make another direct comparison
between lanes 1 and 2. The Results Screen should look like this.
_________________________________________________________________
| Similarity Index = .8000 |
| _______________________________________________________________ |
| DEMO2, Sample 1 DEMO2, Sample 2 |
| Matching Bands = 4 Matching Bands = 4 |
| |
| 1 (1) 2(2) 1 (1) 2 (2) |
| 3 (3) 4(4) 3 (3) 4 (4) |
| |
| Non-Matching Bands = 1 Non-Matching Bands = 1 |
| |
| 5 5 |
| |
-----------------------------------------------------------------
| (1) Return to Main Menu (2) Print (3) Save (4) Match Edit |
| (5) Perform Another Comp. (6) Up (7) Down (8) Notes (9) Map |
-----------------------------------------------------------------
View the map of the comparison by pressing "9". As you can see,
the bands do seem to match up better with the first lane shifted to
the right.
Another way we can change the way the program selects matching
bands is to change the program's sensitivity. There is a margin of
variation allowed for matching pairs. This margin of variation is
based on a percentage of the migration distance of the bands being
compared. The default value has been set at 2.0 percent. Follow
the steps outline below to change the sensitivity of DNA SIMDEX.
1) Return to the Main Menu
2) Press "7", Parameter Set. The Parameter Set Screen will be
displayed.
-----------------Parameter Set------------
| |
| Percent Diff. Allowed for Match = 2 |
| New Percent Diff. Allowed for Match:? |
|__________________________________________|
3) We can make DNA SIMDEX more sensitive by entering a number
lower than 2.0 or less sensitive by entering a number higher than
2.0. The best setting will depend on the gel or autoradiogram we
are analyzing. Let's set the value at 3.0. Type "3.0" <ENTER>.
DNA SIMDEX will not allow bands to be matched that are within 3.0%
of each other.
You have now reviewed all of the major functions of DNA SIMDEX.
Please refer to the manual for a more detailed explanation of the
DNA SIMDEX functions.
