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  • Local pattern searching algorithm

    Hi everyone,

    Does anybody maybe know of a good DNA and/or protein pattern searching algorithm that you can on your local server? I've been looking up a couple of them on the web, but they are all webserver based and also not a variable database. Any help is really appreciated.
    Thanks for reading.

    RickBioinf

  • #2
    You should be able to use "fuzznuc or fuzzpro" from EMBOSS which you can download here: http://emboss.sourceforge.net/download/

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    • #3
      Thanks for the info GenoMax, but unfortunately the link on the website, to download the tool, does not work. Do you have an idea if I can download it in another way?

      Cheers

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      • #4
        Oops, forget it. It is already installed on Bio-linux.

        Thanks again!

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        • #5
          You are all set then.

          On a different note: The EMBOSS link on the open-bio site seems to be redirecting to a lab: http://www.rudloff.se/ which does not seem to have the EMBOSS source code.
          Last edited by GenoMax; 12-18-2013, 07:21 AM.

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          • #6
            Originally posted by GenoMax View Post
            On a different note: The EMBOSS link on the open-bio site seems to be redirecting to a lab: http://www.rudloff.se/ which does not seem to have the EMBOSS source code.
            Which link? Could you report this - eg to the EMBOSS mailing list?

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            • #7
              Originally posted by maubp View Post
              Which link? Could you report this - eg to the EMBOSS mailing list?
              The EMBOSS link under "Main Projects" at http://www.open-bio.org/wiki/Projects is http://emboss.sourceforge.net/ {It was corrected by Peter}. Looks like EMBOSS project lost that domain name.
              Last edited by GenoMax; 12-18-2013, 12:09 PM. Reason: Corrected the EMBOSS link

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              • #8
                Link fixed for now - and I've contacted the EMBOSS guys about the domain name... thanks!

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                • #9
                  Originally posted by maubp View Post
                  Link fixed for now - and I've contacted the EMBOSS guys about the domain name... thanks!
                  Peter: Sorry to revive an old thread but the EMBOSS download appears to be messed up on the EBI mirror. Can you check with your contacts again?

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                  • #10
                    At first glance ftp://emboss.open-bio.org/pub/EMBOSS/ and ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ look OK, but the EBI mirror seems to be lacking some of the folders like the important "old" folder which holds each EMBOSS release. Is that what you meant?

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                    • #11
                      @Peter: You must be seeing a cached version of the ftp site. Clicking on emboss-latest.tar.gz produces a "550 failed to change directory" error.

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                      • #12
                        I would expect that to be a link to the current release, and right now none of the past EMBOSS releases seem to show up on the EBI mirror. I will email the EMBOSS guys.

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