[Bioperl-l] Fwd: BLAST beta, URLAPI, and BioPerl (RemoteBlast users)

Chris Fields cjfields at uiuc.edu
Mon Apr 2 14:10:30 EDT 2007

This may be of interest to anyone using RemoteBlast.

For anyone who uses RemoteBlast, the new changes to NCBI's BLAST  
interface shouldn't affect anything (Scott tested it out).  If there  
are any abnormalities with RemoteBlast queries over the next few  
weeks let us know.


Begin forwarded message:

> From: "Mcginnis, Scott \(NIH/NLM/NCBI\) [E]"  
> <mcginnis at ncbi.nlm.nih.gov>
> Date: April 2, 2007 12:53:33 PM CDT
> To: "Chris Fields" <cjfields at uiuc.edu>
> Subject: RE: BLAST beta, URLAPI, and BioPerl
> Hi Chris:
> We are ready to make the new pages the defaults come April 16th. An  
> announcement is going out shortly. There are some very minor  
> changes to the URL API and I have listed them below. IT will be  
> part of the announcements. Please note we actually tested BioPerl  
> and it seems to me fine with the new pages. If you have a news on  
> your site or a mailing list you might want to pass this on.
> A Note About URLAPI
> The new BLAST pages support URLAPI, a protocol that scripts and
> programs use to run BLAST searches and retrieve results over
> HTTP. (For more on URLAPI, see
> http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html). The following
> information only applies to you if you develop or are responsible
> for software that uses URLAPI.
> The new pages have been tested and produce correct results with
> the following URLAPI client programs:
> * the BioPERL RemoteBlast module
> * the NCBI demo script http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl
> * various scripts used in-house at NCBI
> Users of URLAPI should be aware of the following minor
> changes. In the new interface:
> 1. The Request ID (RID) format will be shorter.  The new format
>     is 11 alphanumeric characters (e.g. RDEFEA5012) and will have no
>     internal structure. The previous RID format was 36 or more
>     characters long, including punctuation (e.g.,
>     1175172712-21345-42512597310.BLASTQ3).
> 2. BLAST reports will show masked regions as lower-case letters
>     by default (see
>     http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W6,
>     figure 2. The current default behavior is to show masked
>     regions as N's or X's. Users may recover the current behavior
>     by adding &MASK_CHAR=0 to the query string for a URLAPI
>     request.
> 3. BLAST reports will show alignments for 100 database sequences
>     by default. The current reports show only 50 alignments by
>     default.
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 3/5/2007 11:50 AM
> To: Mcginnis, Scott (NIH/NLM/NCBI) [E]
> Subject: BLAST beta, URLAPI, and BioPerl
> The BioPerl project has several have several modules and parsers
> which currently parse XML/text/tabular BLAST output, as well as a
> module which is capable of posting BLAST queries via the URLAPI
> interface.  Will any of the BLAST changes affect these (particularly
> Thanks!
> chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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