Page 1 of 2 12 LastLast
Results 1 to 10 of 19

Thread: Furutrad DNA tools - Chromosome 2D visualizer and comparison software

Hybrid View

Previous Post Previous Post   Next Post Next Post
  1. #1
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    Lightbulb Furutrad DNA tools - Chromosome 2D visualizer and comparison software

    Hi!

    I am developing an experiment software that visualize your Autosomal result as a 2D picture. There are some built-in comparison possibilities. The tool (for Windows) is under development and can be downloaded from here:


    The chromosome visualization is basically a 4-way approach:
    1. Divide the chromosome into 4 strings of A, C, G and T's of equal length.
    2. Fold the strings like a 2D square using Hilbert space-filling curve algorithm.
    3. Apply various imageprocessing filters and pattern recognition algorithms on the squares.
    4. Apply colors to the squares using different presets.


    The patterns themselves does not tell you anything, they are meaningless. The purpose is to find a way of comparing and finding matching patterns between autosomal kits, but the patterns is more like admixture finding than matching autosomal segments.

    Here is a screenshot of the software:



    Here is my 22 chromosomes visualized in one picture (Left: A, C and G. Right: C, G and T):



    ... so now you have the possibility to add a graphical version of your DNA to your profile

  2. The Following 2 Users Say Thank You to PeterLarsen For This Useful Post:

     everest59 (03-08-2014),  MfA (03-08-2014)

  3. #2
    Registered Users
    Posts
    2,681
    Sex
    Location
    New York
    Ethnicity
    South Asian
    Nationality
    American
    Y-DNA (P)
    J2b2-M241 (J-Y978*)
    mtDNA (M)
    M30b2a
    Y-DNA (M)
    R1a1-L657 (R-Y16494)
    mtDNA (P)
    M18a

    United States of America Canada
    How do we interpret the comparisons? And can you tell us more about the virtual child and random child options?
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

  4. #3
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    The comparisons is done by comparing the resulting 2D image, it is a summarization of all differences. The whole idea is to get away from the 1d line comparisons that standard autosomal comparisons is made and instead compare overall patterns. It is more an admixture comparison than an "related with" comparison.

    The virtual child mixes up DNA from both autosomal exports selected and generates a new one. It takes allele information in segments of random length from the "parents" and generates a new .csv-file. There is nothing special about it, just a simple combining algorithm.

    Random child is currently unavailable. It is supposed to work like the virtual child although you need only to select one parent and from that it generates a new child where half the alleles is from the parent and other half is random. The random part is difficult, as SNP's isn't truly random so I need to apply some sort of probabilistic table and connect it to SNPedia (or something similar) to make it useful.

    Most effort is actually put into the all chromosome visualizer, the comparison algorithm isn't that great as of yet which can easily be verified by generating a virtual child and the overall difference between a parent and a virtual child is often larger than comparing two unrelated autosomal exports.
    Last edited by PeterLarsen; 03-08-2014 at 11:29 AM.

  5. #4
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    Quote Originally Posted by PeterLarsen View Post
    ....
    Most effort is actually put into the all chromosome visualizer, the comparison algorithm isn't that great as of yet which can easily be verified by generating a virtual child and the overall difference between a parent and a virtual child is often larger than comparing two unrelated autosomal exports.
    I think I need to elaborate on the above statement. The purpose of the visualizer was to create human recognizeable patterns, eye-candy, so that all you see isn't only a picture of dots but distinct patterns. How the pattern algorithm now works: small differences in the allele leads to huge impacts on the generated patterns (it wouldn't be fun all having a similar looking picture), does have negative impact on the comparison algorithm. I will sooner or later add functionality to compare "non-patternized" 2D visualizations that will actually compare areas on the autosomal chromosomes 2d visualizations, and that will be of greater interests in comparing the overall structure.

    As the focus now is on eye-candy patterns, the comparison algorithm suffers. It will soon be options to focus on either one: eye-candy or functional.
    Last edited by PeterLarsen; 03-08-2014 at 12:34 PM.

  6. #5
    Registered Users
    Posts
    2,681
    Sex
    Location
    New York
    Ethnicity
    South Asian
    Nationality
    American
    Y-DNA (P)
    J2b2-M241 (J-Y978*)
    mtDNA (M)
    M30b2a
    Y-DNA (M)
    R1a1-L657 (R-Y16494)
    mtDNA (P)
    M18a

    United States of America Canada
    When I try to use the all chromosome visualizer, I get an error: "unhandled exception has occurred in your application" .. "index was out of range" ... "parameter name: index"

    See the end of this message for details on invoking
    just-in-time (JIT) debugging instead of this dialog box.

    ************** Exception Text **************
    System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection.
    Parameter name: index
    at System.ThrowHelper.ThrowArgumentOutOfRangeExceptio n()
    at System.Collections.Generic.List`1.get_Item(Int32 index)
    at WindowsFormsApplication1.Form1.RemoveAutosomalNotS hared(autosomal a1, autosomal a2, String chr)
    at WindowsFormsApplication1.Form1.visualizeChromosome (Int32 iChr, Int32 vType)
    at System.Windows.Forms.Control.OnClick(EventArgs e)
    at System.Windows.Forms.Button.OnMouseUp(MouseEventAr gs mevent)
    at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
    at System.Windows.Forms.Control.WndProc(Message& m)
    at System.Windows.Forms.ButtonBase.WndProc(Message& m)
    at System.Windows.Forms.Button.WndProc(Message& m)
    at System.Windows.Forms.Control.ControlNativeWindow.W ndProc(Message& m)
    at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)


    ************** Loaded Assemblies **************
    mscorlib
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5472 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/Microsoft.NET/Framework64/v2.0.50727/mscorlib.dll
    ----------------------------------------
    Furutrad14
    Assembly Version: 1.0.0.1
    Win32 Version: 1.0.0.1
    CodeBase: file:///C:/Users/McNinja/AppData/Roaming/Microsoft/Windows/Start%20Menu/Programs/Furutrad%20-%20artificial.se/Furutrad14.exe
    ----------------------------------------
    System.Windows.Forms
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5468 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Windows.Forms/2.0.0.0__b77a5c561934e089/System.Windows.Forms.dll
    ----------------------------------------
    System
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5467 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System/2.0.0.0__b77a5c561934e089/System.dll
    ----------------------------------------
    System.Drawing
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5467 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Drawing/2.0.0.0__b03f5f7f11d50a3a/System.Drawing.dll
    ----------------------------------------

    ************** JIT Debugging **************
    To enable just-in-time (JIT) debugging, the .config file for this
    application or computer (machine.config) must have the
    jitDebugging value set in the system.windows.forms section.
    The application must also be compiled with debugging
    enabled.

    For example:

    <configuration>
    <system.windows.forms jitDebugging="true" />
    </configuration>

    When JIT debugging is enabled, any unhandled exception
    will be sent to the JIT debugger registered on the computer
    rather than be handled by this dialog box.

    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

  7. #6
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    Quote Originally Posted by Dr_McNinja View Post
    When I try to use the all chromosome visualizer, I get an error: "unhandled exception has occurred in your application" .. "index was out of range" ... "parameter name: index"
    Oh great thanks!, I will look into that right away. Seems like there is an issue with the kit selector

  8. #7
    Registered Users
    Posts
    2,681
    Sex
    Location
    New York
    Ethnicity
    South Asian
    Nationality
    American
    Y-DNA (P)
    J2b2-M241 (J-Y978*)
    mtDNA (M)
    M30b2a
    Y-DNA (M)
    R1a1-L657 (R-Y16494)
    mtDNA (P)
    M18a

    United States of America Canada
    But how do we tell if the image from one kit bears a greater or lesser resemblance to a third kit than another? It just comes out looking like random colorful noise.

    So would using the virtual child function multiple times result in slightly different results each time?
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

  9. #8
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    Quote Originally Posted by Dr_McNinja View Post
    But how do we tell if the image from one kit bears a greater or lesser resemblance to a third kit than another? It just comes out looking like random colorful noise.

    So would using the virtual child function multiple times result in slightly different results each time?
    There is a textfield below the picture area where you can read the resulting differences between two kits chromosome. Yes, the virtual child option creates different childs every time even if the same parents is chosen because the inherited segment lengths is random.

  10. #9
    Registered Users
    Posts
    2,681
    Sex
    Location
    New York
    Ethnicity
    South Asian
    Nationality
    American
    Y-DNA (P)
    J2b2-M241 (J-Y978*)
    mtDNA (M)
    M30b2a
    Y-DNA (M)
    R1a1-L657 (R-Y16494)
    mtDNA (P)
    M18a

    United States of America Canada
    The single chromosome comparison works, but I'm not sure why the 'Total diff all' value is higher with a virtual/phased child than it is to the other parent kit. It was 477k between me and the child (481k between other kit and child) and 474k between me and the other kit. How is that possible?
    Last edited by Dr_McNinja; 03-08-2014 at 01:15 PM.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

  11. #10
    Registered Users
    Posts
    11
    Sex
    Y-DNA (P)
    I1 >Z382 ... >Y18238
    mtDNA (M)
    Z1a1a

    Quote Originally Posted by Dr_McNinja View Post
    The single chromosome comparison works, but I'm not sure why the 'Total diff all' value is higher with a virtual/phased child than it is to the other parent kit. It was 477k between me and the child (481k between other kit and child) and 474k between me and the other kit. How is that possible?
    That is possible because of how the patterns is created. Depending on how the ACGT is structured any difference creates huge impact on the generated pattern. When using the "Solid" option, it will be more useful for comparisons but so far the comparisons only works on the patternized 2D visualizations. I tend to activate comparisons using the "Solid" visualizations as soon as the area comparison algorithm works better.

    I tried fix the bug you found, version 1.14b is now available for download.
    Last edited by PeterLarsen; 03-08-2014 at 02:03 PM.

Page 1 of 2 12 LastLast

Similar Threads

  1. Anyone using Gedmatch for X chromosome comparison?
    By IrishTypeIII in forum X Chromosome (X-DNA)
    Replies: 2
    Last Post: 06-29-2017, 12:01 AM
  2. Replies: 1
    Last Post: 05-03-2017, 02:46 AM
  3. Replies: 5
    Last Post: 04-20-2017, 04:24 AM
  4. YHap software
    By Ann Turner in forum Other
    Replies: 0
    Last Post: 04-12-2013, 01:46 PM
  5. Easy to Use DNA Software
    By Ian B in forum General
    Replies: 2
    Last Post: 03-14-2013, 02:04 AM

Tags for this Thread

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •