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 include: * 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: http://bioinf.dimi.uniud.it/software The technical report describing the underlying algorithms is also available. Any comments are welcome. Regards Nicola Vitacolonna -- ** ** Get my GPG public key at: ** * ** * www.dimi.uniud.it/~vitacolo ** * ** * or finger vitacolo at dimi.uniud.it ** * Università degli Studi di Udine * ***icola Vitacolonna