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Question regarding SSAHA

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  • Kelvin Low Kong Gui
    Hello there, We are now conducting a research on DNA searching algorithm under the Windows environment. I would like to find out is there a copy of SSAHA for
    Message 1 of 5 , Apr 12, 2006
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      Hello there,

      We are now conducting a research on DNA searching algorithm under the
      Windows environment. I would like to find out is there a copy of SSAHA
      for Windows? Or is there anyway I can run the current SSAHA under
      Windows?

      Plese advice. Thank you.


      Regards,
      Kelvin
    • Adam Spargo
      Hi, SSAHA is open source so you can try to compile it yourself for windows. SSAHA2 is better but unfortunately we have can t yet make it open source. I don t
      Message 2 of 5 , Apr 12, 2006
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        Hi,
        SSAHA is open source so you can try to compile it yourself for windows.
        SSAHA2 is better but unfortunately we have can't yet make it open source.
        I don't have a windows machine to build it on.

        You should be aware that you need number_of_bases/3 to store the hash plus
        number_of_bases if you want to keep the sequence in memory. So for the
        human genome say, you need at least 4 or 5 GB, this is why we assume
        people will use a unix/linux OS.

        Adam.




        On Wed, 12 Apr 2006, Kelvin Low Kong Gui wrote:

        > Hello there,
        >
        > We are now conducting a research on DNA searching algorithm under the
        > Windows environment. I would like to find out is there a copy of SSAHA
        > for Windows? Or is there anyway I can run the current SSAHA under
        > Windows?
        >
        > Plese advice. Thank you.
        >
        >
        > Regards,
        > Kelvin
        >
        >
        >
        >
        >
        >
        > Yahoo! Groups Links
        >
        >
        >
        >
        >
        >
        >
        >

        --
        Dr Adam Spargo
        High Performance Assembly Group email: aws@...
        Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
        Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
      • Anthony Cox
        Hello Kelvin Don t know about SSAHA2, but the source code for SSAHA version 3.1 could be compiled under Windows by installing Cygwin, making sure you include
        Message 3 of 5 , Apr 12, 2006
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          Hello Kelvin

          Don't know about SSAHA2, but the source code for SSAHA
          version 3.1 could be compiled under Windows by
          installing Cygwin, making sure you include gcc/g++ in
          the installation. However the resulting executable is
          only runnable under the Cygwin environment.

          Or check out MinGW/Msys - advantage of this approach
          is that the executable would be runnable from Windows.



          --- Kelvin Low Kong Gui <geex20@...> wrote:

          > Hello there,
          >
          > We are now conducting a research on DNA searching
          > algorithm under the
          > Windows environment. I would like to find out is
          > there a copy of SSAHA
          > for Windows? Or is there anyway I can run the
          > current SSAHA under
          > Windows?
          >
          > Plese advice. Thank you.
          >
          >
          > Regards,
          > Kelvin
          >
          >
          >
          >
          >
          >
          > Yahoo! Groups Links
          >
          >
          > ssahausers-unsubscribe@yahoogroups.com
          >
          >
          >
          >
          >
          >


          Send instant messages to your online friends http://uk.messenger.yahoo.com
        • Kong Gui (gs'20)
          Hello, Thank you for your advices. I will try to work on it. Will post additional question here if I bump into any obstacles. Once again, thank you. Cheers,
          Message 4 of 5 , Apr 12, 2006
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            Hello,
             
            Thank you for your advices. I will try to work on it. Will post additional question here if I bump into any obstacles. Once again, thank you.
             
            Cheers,
            Kelvin

            Send instant messages to your online friends http://uk.messenger.yahoo.com

          • Kong Gui (gs'20)
            Hello Anthony, Regarding the suggestion on compiling SSAHA under MinGW/Msys, will you please guide me through the compilation? For now, I ve had both
            Message 5 of 5 , Apr 13, 2006
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              Hello Anthony,
               
              Regarding the suggestion on compiling SSAHA under MinGW/Msys, will you please guide me through the compilation?
               
              For now, I've had both MinGW/Msys installed under C:. But I can't figure how am I going to use them to compile SSAHA. What I did so far was, by turning on the Msys terminal and locate the directory of "SSAHA/binary", following by the command "make makefile". But it doesn't seem to work with me over here.
               
              Any hints? Thank you very much.
               
              Regards,
              Kelvin
              Student.


              Anthony Cox <anthony.j.cox@...> wrote:
              Hello Kelvin

              Don't know about SSAHA2, but the source code for SSAHA
              version 3.1 could be compiled under Windows by
              installing Cygwin, making sure you include gcc/g++ in
              the installation. However the resulting executable is
              only runnable under the Cygwin environment.

              Or check out MinGW/Msys - advantage of this approach
              is that the executable would be runnable from Windows.

              Send instant messages to your online friends http://uk.messenger.yahoo.com

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