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inquiry for bioperl Rose 03-04-2008
Posted by Rose on March 4, 2008, 9:35 am
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 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)?



Posted by smallpond on March 4, 2008, 12:17 pm
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> 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

Posted by Uri Guttman on March 4, 2008, 1:21 pm
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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

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Posted by xhoster on March 4, 2008, 3:44 pm
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> 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

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