Bioperl/ANNOUNCE interactive perl shell / Webblast v0.97 / Recent posts

Georg Fuellen
Tue, 25 May 1999 22:44:46 +0200 (MET DST)

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1: interactive perl shell (psh)... (Bob MacCallum)
2: Webblast v0.97, an update to use blast 2.08 at NCBI (Dong Li (Alex))
3: Recent posts to our discussion lists (Georg Fuellen)


Date: Tue, 18 May 1999 10:49:24 +0100
From: Bob MacCallum <>
Subject: interactive perl shell (psh)...

hello bioperlers,

well i've been sitting on this for some time now because i live in fear of
people actually using my code and emailing me all the time...

it's just a simple interactive perl shell (psh) which marcel turcotte (also
at the ICRF) and i developed about a year ago. with GNU ReadLine correctly
installed it gives full command-line editing, up-down history and
command/filename/variable/hash/subroutine name completion

i think some of you might find it useful to use BioPerl modules and objects
in real time (and maybe end up with something a bit like the Darwin

it also provides full access to unix commands/programs using perl syntax,
of course.  so you can do for example:
psh> ls '/etc', '/var';  # clever stuff...

i use it most of all for prototyping bits of code, or things like renaming
lots of files. but it hasn't replaced tcsh for me.  i know there are other
perl shells out there too.

if anyone is interested just email me and i'll send you the psh script and
a sample .pshrc [please allow 28 hours for delivery]

you will need the following installed (or later versions):

* perl 5.004 (i think 5.003 will work)
* GNU Readline Library 2.1 (C library)
* Term-ReadLine-Gnu-1.01 (Perl interface from CPAN)

please direct any follow-up to the non-announce list, to which i will stay
subscribed for a little while.  

hope to hear from you,


           bob maccallum [phd] : email
        biomolecular modelling lab : imperial cancer research fund
              44 lincoln's inn fields : london wc2a 3px : uk
             telephone +44 171 269 3405 : fax +44 171 269 3258


Date: Thu, 20 May 1999 21:53:29 -0400
From: "Dong Li (Alex)" <>
Subject: Webblast v0.97, an update to use blast 2.08 at NCBI

Hello, there,

If you have been using webblast v0.94, you may want to get the new version
of webblast v0.97, which is updated to use blast v2.0.8 at NCBI, from the
following URL:

Here is the list of new features: 
1) the sequences longer than the maximum length will be splitted first and
the smaller fragments will be used to blast. To disable automatic
splitting, add 
2) new option "-overlap=integer" sets the overlapping length of smaller
fragments if the long sequences are splitted.
3) new option "-organism=name|number_representation" allows to limit
database for searching. 
4) new option "-matrix=number_representation" allow to use a different
scoring matrix. 
5) updated to use new version 2.0.8 of BLAST at NCBI. 

This new improved verion should be back version compatible if the new option 
"-split=off" is used and maximum length is set to 30000 (default is 10000
now to minimize occurrence of "CPU limit reached"). 

Here is the list of some other features: 
1) runs on all unix, Windows NT/9x--see installation instructions in the file. 
2) very easy to install; 
3) can retrieve the graphical overview; 
4) some useful options: -default (same as -notask), -silent, -help, -test -log 
5) Some important options are available in interactive mode; 
6) can use list file. 

To get help, enter "webblast -help".



ICQ #: 30246871


Date: Tue, 25 May 1999 22:40:10 +0200 (MET DST)
From: Georg Fuellen <fuellen>
Subject: Recent posts to our discussion lists

Hello everyone,

To keep you informed, here's a selected list of threads going
on over the last few weeks on our discussion lists:

      Bioperl: XML Vicki Brown 
      Bioperl: Alignment factories Ian Holmes 
      Bioperl: Bioperl 99 - Credit Cards now accepted Ewan Birney 
      Bioperl: Announcing: PerlMonth (new web-based Perlzine) Vicki Brown 
      Bioperl: read scf file olivier DUGAS 
      Bioperl: Parser of genbank features (and swissprot and ...) Rubin Eitan 
      Bioperl: CORBA vs XML Ewan Birney 
      Bioperl: blast_seq issues James Diggans 
      Bioperl: NCBI 'Query' email server Simon Twigger 
      Bioperl: Announce: xml-mol mail list adam moore

      Bioperl-guts: Collaborating packages... Ewan Birney 
      Bioperl-guts: Entry object interface 
      Bioperl-guts: standard feature set (fwd) Ian Holmes 
      Bioperl-guts: Streamable interfaces Ewan Birney 
      Bioperl-guts: Please come to YAPC Kevin Lenzo 
      Bioperl-guts: Re: interface definitions Aaron J Mackey 
      Bioperl-guts: Search stuff... Ewan Birney 
      Bioperl-guts: implementation in the interfaces Ewan Birney 
      Bioperl-guts: Search try #2 Aaron J Mackey 
      Bioperl-guts: Bio::SeqIO::SCF done. Aaron J Mackey 
      Bioperl-guts: SeqFeature/GFF compatibility Ewan Birney 
      Bioperl-guts: Intent to make a Debian/Linux package of BioPerl 
        Stephane Bortzmeyer 
      Bioperl-guts: Bio::RangeI and Bio::Range Matthew Pocock 
      Bioperl-guts: Bio::DB::BioSeqI and efficiency, late binding, etc. 
        Mr P.A. Van Heusden 
      Bioperl-guts: SeqFeatures Matthew Pocock 
      Bioperl-guts: commits on SeqFeature Ewan Birney 
      Bioperl-guts: SeqFeatures Matthew Pocock 

Thanks a lot to all contributors!

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