Logic Alignment Free (LAF)

A new classification technique for biological sequences called LAF is introduced: the combination of alignment free k-mer frequency counts and logic data mining allows the analysis of biological sequences without the strict requirement of an alignment or of an overlapping DNA gene region. This leads to the possibility of performing classification of non coding DNA, which is not alignable, and of whole genomes, which are very hard to align, as the problem of whole genome alignment is computationally hard. The performed experiments show that this technique is very promising in distinguishing functional versus non functional elements inside the same organism and in classifying diverse organisms whole genomes at different levels of the phylogenetic tree.

LAF software

Data sets

LAF utilities