[BioRuby] Fwd: [blast-announce] [BLAST-Announce #59] New BLAST design to be released on April 16, 2007

[Toshiaki Katayama]

Hi,

NCBI announced that their BLAST interface will change.
Currently, BioRuby does not support remote BLAST on NCBI server (we have remote BLAST on GenomeNet and SOAP access for DDBJ BLAST service, instead).
Are there anyone working on the NCBI's URLAPI?

Toshiaki

Begin forwarded message:

> From: "Mcginnis, Scott (NIH/NLM/NCBI) [E]" <mcginnis at ncbi.nlm.nih.gov>
> Date: 2007年4月3日 2:57:48:JST
> To: <blast-announce at ncbi.nlm.nih.gov>
> Subject: [blast-announce] [BLAST-Announce #59] New BLAST design to be released on April 16, 2007
>
> April 2, 2007: New BLAST design to be released on April 16, 2007
> ----------------------------------------------------------------
>
> The new NCBI BLAST pages will become the default interface at
> http://ncbi.nlm.nih.gov/blast on April 16, 2007. The new
> interface is currently available as a beta release at
> http://ncbi.nlm.nih.gov/blast/beta/.  For details on the new
> interface, see http://www.ncbi.nlm.nih.gov/BLAST/beta/about/.
>
> After the new interface is released, the previous interface will
> remain available from a link on the new front page until May 14,
> 2007.
>
> 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. 
>
> If you have any questions please send them to mcginnis at ncbi.nlm.nih.gov