[announcement] Discontiguous MegaBLAST at NCBI

George Coulouris coulouris at ncbi.nlm.nih.gov
Mon Aug 18 08:59:47 EST 2003

Now available on the NCBI BLAST web pages is a new type of nucleotide
search called Discontiguous MegaBLAST:


Like MegaBLAST, this service uses a greedy algorithm and concatenates
queries to save time scanning the databases. But instead of using
exact matches to database sequences for initial hits, it finds matches
to a discontiguous template made from the query. This results in fewer
initial words but more statistically significant alignments. This
makes Discontiguous MegaBLAST good for comparison of divergent
sequences, especially from different organisms, which have alignments
with low degree of identity but perhaps encode similar proteins.

Discontiguous MegaBLAST can be found on the main NCBI BLAST web page at


It is also included in the WWW BLAST server located at:

Discontiguous MegaBLAST searches can also be done using Standalone
BLAST. To do this, you can specify in the megablast binary, template
length option, with the -t parameter and the Template Type with
parameter -N. The word size (-W) must also be set to 11 or 12 for
Discontiguous MegaBLAST seaches.

For any questions please contact blast-help at ncbi.nlm.nih.gov.

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