[Next-Generation Sequencing Book]
  • [Photo] Scott D. McGinnis • April 3, 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:
    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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