inquiry for bioperl

Discussion in 'Perl Misc' started by Rose, Mar 4, 2008.

  1. Rose

    Rose Guest

    Dear all,

    Since I'm unable to identify a newsgroup at bioperl, i post a message here.
    Please tell me if I should post this somewhere else. Are bioperl modules
    capable of handling genomes (characters of larger than 4M or even giga)?
    Rose, Mar 4, 2008
    #1
    1. Advertising

  2. Rose

    smallpond Guest

    On Mar 4, 9:35 am, "Rose" <> wrote:
    > Dear all,
    >
    > Since I'm unable to identify a newsgroup at bioperl, i post a message here.
    > Please tell me if I should post this somewhere else. Are bioperl modules
    > capable of handling genomes (characters of larger than 4M or even giga)?



    bioperl looks like a very interesting project. perl certainly can
    deal with
    large data files. If the bioperl modules are like CPAN modules, it is
    probably
    best to check the documentation for each module that you want to use
    on what
    it's limits are. This article:

    http://www.bioperl.org/wiki/How_Perl_saved_human_genome

    seems to imply that bioperl is used on 3G sequences. The article is
    pretty good
    except for the wrong-headed decision not to use pTk.
    --S
    smallpond, Mar 4, 2008
    #2
    1. Advertising

  3. Rose

    Uri Guttman Guest

    >>>>> "R" == Rose <> writes:

    R> Since I'm unable to identify a newsgroup at bioperl, i post a
    R> message here. Please tell me if I should post this somewhere
    R> else. Are bioperl modules capable of handling genomes (characters
    R> of larger than 4M or even giga)?

    i doubt you will find many bioperl users in this newsgroup. i can't
    recall ever seeing it discussed here as it is a very specialized package.

    bioperl has its own mailing list. you can subscribe to it from this page:

    http://lists.cpan.org/showlist.cgi?name=bioperl-l

    uri

    --
    Uri Guttman ------ -------- http://www.sysarch.com --
    ----- Perl Architecture, Development, Training, Support, Code Review ------
    ----------- Search or Offer Perl Jobs ----- http://jobs.perl.org ---------
    --------- Gourmet Hot Cocoa Mix ---- http://bestfriendscocoa.com ---------
    Uri Guttman, Mar 4, 2008
    #3
  4. Rose

    Guest

    "Rose" <> wrote:
    > Dear all,
    >
    > Since I'm unable to identify a newsgroup at bioperl, i post a message
    > here. Please tell me if I should post this somewhere else. Are bioperl
    > modules capable of handling genomes (characters of larger than 4M or even
    > giga)?


    BioPerl covers a lot of different functionalities. I think that at least
    some of them will *not* be able to handle gigabases, while others will be
    able to (provided your hardware is up to it--what do you have?).

    There hasn't been much BioPerl traffic here in the past. That community
    seems to prefer mailing lists and wikis over usenet, see
    http://www.bioperl.org/wiki/Main_Page



    Xho

    --
    -------------------- http://NewsReader.Com/ --------------------
    The costs of publication of this article were defrayed in part by the
    payment of page charges. This article must therefore be hereby marked
    advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate
    this fact.
    , Mar 4, 2008
    #4
    1. Advertising

Want to reply to this thread or ask your own question?

It takes just 2 minutes to sign up (and it's free!). Just click the sign up button to choose a username and then you can ask your own questions on the forum.
Similar Threads
  1. Debashish
    Replies:
    3
    Views:
    1,804
    Mike Treseler
    Aug 8, 2003
  2. Leon Shaw

    Databinding Inquiry

    Leon Shaw, Jul 11, 2003, in forum: ASP .Net
    Replies:
    1
    Views:
    374
    Leon Shaw
    Jul 11, 2003
  3. Joe Van Meer

    data relations and datasets inquiry

    Joe Van Meer, May 5, 2004, in forum: ASP .Net
    Replies:
    0
    Views:
    425
    Joe Van Meer
    May 5, 2004
  4. Replies:
    1
    Views:
    10,413
    kj12345
    Mar 1, 2005
  5. Shuo Xiang

    [OT]GTKmm toolkit inquiry

    Shuo Xiang, Jul 17, 2003, in forum: C++
    Replies:
    1
    Views:
    341
    Jim Fischer
    Jul 17, 2003
Loading...

Share This Page