[BiO BB] Fwd: Discontiguous MegaBLAST

Joseph Landman landman at scalableinformatics.com
Fri Aug 15 11:50:19 EDT 2003

-----Forwarded Message-----
Date: 15 Aug 2003 10:56:28 -0400

Now available on the NCBI BLAST web pages is a new type of nucleotide search
called Discontiguous MegaBLAST
(http://www.ncbi.nlm.nih.gov/blast/discontiguous.html). 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. 

Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman at scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615

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