[Biodevelopers] SMaRTFinder

Nicola Vitacolonna vitacolo at dimi.uniud.it
Wed Nov 12 04:31:04 EST 2003

Just to let you know that we have written a quite efficient program, called 
SMaRTFinder, to search for structured motifs (lists of motifs at relative 
distances specified by intervals) in biosequences. The program is a command 
line tool, still under development, but fully functional. Its features 

* finding occurrences exactly or approximately
* finding partial matches (i.e., matches made of only a fraction of all the 
component patterns)
* working with DNA, RNA, IUPAC, protein and ASCII alphabets
* allowing classes of characters
* searching one or both strands of a DNA sequence
* using Kurtz's implementation of lazy suffix trees

Currently, SMaRTFinder reads only files in FASTA format, and outputs a file 
in GFF format (to be visualized with programs like Apollo Genome Browser). We 
are working on a graphical interface.

Source code (ISO C++) and binaries for some platforms are available here:


The technical report describing the underlying algorithms is also available.

Any comments are welcome.

Nicola Vitacolonna
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