NCBI BLAST beta to become default

Just following up on a previous post, the new NCBI BLAST design becomes the default from April 16. Read more for the details from Scott. Good to see specific mention of the Bioperl RemoteBlast module.

April 2, 2007: New BLAST design to be released on April 16, 2007
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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@ncbi.nlm.nih.gov.

One thought on “NCBI BLAST beta to become default

  1. Chris Fields

    We have been communicating with NCBI on and off to make sure there wouldn’t be problems. Scott McGinnis was very helpful in making sure RemoteBlast worked with the URLAPI changes. Nice to know they’re thinking about us!

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