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The present special issue of GMR includes selected papers from the X-meeting 2006, held in Fortaleza, CE, Brazil, together with the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006). Dr. Goran Neshich, EMPRAPA, chaired this seminal event for the Brazilian bioinformatics community, co-chaired by Dr. Ana Tereza R. Vasconcelos from LNCC. The X-meeting is the annual meeting of the AB3C (Associaçao Brasileira de Bioinformática e Biologia Computacional), which is the regional group affiliated with the International Society for Computational Biology (ISCB). Thus, AB3C has reached maturity as a Brazilian association engaged in the progress of bioinformatics and has therefore attained international recognition.