Loading ...
Sorry, an error occurred while loading the content.
 

Question regarding SSAHA

Expand Messages
  • 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
      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
        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
          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
            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
              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

            Your message has been successfully submitted and would be delivered to recipients shortly.