[Bioperl-l] remote ncbi blast

Jonathan Epstein Jonathan_Epstein@nih.gov
Wed, 04 Apr 2001 16:54:33 -0400

At 04:07 PM 4/4/2001 , Jason Stajich wrote:
>Remote blast (Bio::Tools::Blast) has been broken with the changes to ncbi
>blast for about 9 months or so.  I propose we still try and support it, at
>first at least through NCBI's blastcl3 tool which is available for almost
>all platforms including macintosh.  It is possible to use it just like
>blastall except that it connects to remote blast server queue and requests
>the job.  Supporting this would require minor changes to StandAloneBlast
>to call the blastcl3 application.  Would this be an acceptable solution
>for people?

This would be great from my viewpoint, Jason.

>While we're on the topic of remote NCBI resources and to toast Heikki's
>Bio::DB::EMBL. I'd like to think about the relative un-reliable nature of
>Bio::DB::GenBank much of the time.  At least when running the tests I
>often get problems with the DB.t tests when running the GenBank/GenPept
>queries.  I'm not sure if this is just the proximity of the queries
>causing NCBI to rehect them, bad network connections, or what.  I've been
>playing with ncbi network entrez which is available as mac/windows/unix
>executables which is always reliable.  Is there any easy way to take
>advantage of their TCP/IP connection approach.  I know there is probably
>some wicked ASN1.1 going on underneath, but it is reliable and fast...

Actually the ASN.1 isn't wicked, it's great!  However, I can probably help 
you with it.  The problem is: do you want to use a simple command-line 
program such as Nentrcmd to run underneath the Perl code, or do you want to 
actually link in portions of the NCBI toolkit via XS, etc.?  The latter has 
a lot of pluses and minuses:
+ faster
+ opens up other portions of the NCBI toolkit for access from BioPerl 
(e.g., the blast API)
- much more difficult to implement
- adds additional complexities and dependencies to installation of BioPerl


Jonathan Epstein                                Jonathan_Epstein@nih.gov
Head, Unit on Biologic Computation              (301)402-4563
Office of the Scientific Director               Bldg 31, Room 2A47
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National Institutes of Health                   Bethesda, MD 20892