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  • Repbase needed

    I've registered 3 times at Giri in the last month in order to download Repbase repeatmasker edition. I have yet to get a confirmation. Can anyone share their copy, or shoot me a link to an alternate download? I really need to get this project moving.

    Much appreciated!!

  • #2
    IIRC you can get repbase from the FTP site at EBI.

    Comment


    • #3
      The versions of repbase you'll find on public FTP sites will be older versions from before GRI started to commercialise it, which was a few years back now. We still use the public version for repeatmasker filtering, but newer versions will have advantages for some applications.

      This is another one of those databases (like transfac before it) which are crying out for a renewed public, free implementation to be put together.

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      • #4
        Originally posted by k-gun12 View Post
        I've registered 3 times at Giri in the last month in order to download Repbase repeatmasker edition. I have yet to get a confirmation. Can anyone share their copy, or shoot me a link to an alternate download? I really need to get this project moving.

        Much appreciated!!
        Check your Spam mail. I had this problem a couple of years ago and realized all the responses from GIRI were getting filtered. There is not much text in the messages they send, just two links and a computer generated password. Guess it looks like spam.

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        • #5
          Nothing in the spam.. but I did wind up getting access. I just used the 'forgot password' link with an email I registered with and finally got an email.

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          • #6
            Hi, I don't suppose you could send me a link where I could download the public older versions of Repbase?

            Thanks

            Alex

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            • #7
              ftp://ftp.ebi.ac.uk/pub/databases/repbase/

              Comment


              • #8
                Is anyone using this?

                I tried to get an account, but they didn't send me a password. I already tried several times to get in contact via e-mail, but I never got a reply.

                Does anyone know a way how I could access to this database? Or is there maybe a good alternative that I could use to annotate the transposable elements of the genome I'm working on?

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                • #9
                  Originally posted by AnneH View Post
                  Is anyone using this?

                  I tried to get an account, but they didn't send me a password. I already tried several times to get in contact via e-mail, but I never got a reply.

                  Does anyone know a way how I could access to this database? Or is there maybe a good alternative that I could use to annotate the transposable elements of the genome I'm working on?
                  It is hard to offer specific advice because we don't know which genome you are working on.
                  Do you have an assembled genome, or just WGS reads? Is this closely related to a model species?

                  In reference to the password issue, did you see the suggestions above? Specifically, check your spam folder. They send a response that always seems to get filtered, and as others said, it might not be sent immediately. Make sure you are registered and using the correct email, then try again. I've forgotten my password a number of times, but never had any access issues with RepBase.

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                  • #10
                    I'm working on an assembled fungal genome. The fungus is a basidiomycete. I'm not sure about close relations to model species, but Ustilago maydis might be closest.

                    I checked my Spam-Folder, there was nothing. And I also tried to go via the forgot password page. When I enter my email address, it says, they sent me the new password, but again nothing in my emails/spam.
                    I even sent an email to webmaster and database administrator, but I didn't get any replies :-/

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                    • #11
                      Originally posted by AnneH View Post
                      I'm working on an assembled fungal genome. The fungus is a basidiomycete. I'm not sure about close relations to model species, but Ustilago maydis might be closest.

                      I checked my Spam-Folder, there was nothing. And I also tried to go via the forgot password page. When I enter my email address, it says, they sent me the new password, but again nothing in my emails/spam.
                      I even sent an email to webmaster and database administrator, but I didn't get any replies :-/
                      Just a thought, are you using an academic email address? I think there might be some restrictions on the use of the database, so perhaps your address is being ignored. I'm not sure this helps, but hopefully you find a solution. As I said previously, I've never experienced these issues.

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                      • #12
                        Yes, I'm using an academic email address. It's a pity, but maybe I will find another way to find my TEs.

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                        • #13
                          Originally posted by AnneH View Post
                          Yes, I'm using an academic email address. It's a pity, but maybe I will find another way to find my TEs.
                          What is your end goal with the analysis? For example, do you want to create fine scale annotations of full-length TEs, or simply find the relative abundance of different TE types? If it is the latter, you can do that from the raw reads (but you will need a reference set of TEs of some sort). For annotation of TEs in a reference genome there are a number of good programs that will find elements based on structure and similarity, but this is a much more involved and tedious procedure. It really depends on what you want to know about the TEs.

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