[Biopython-dev] Changes in BLAST URLAPI

[Sebastian Bassi]

I wonder if net blast would be affected by this change (from April 16,
according to BLAST newsletter):

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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

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