Description of the method to estimate the length of the terminal-fragment size for partial 16S rRNA sequences. The closest sequences (by homology search) in the RDP database are used to estimate the length of the fragment and its phylogenetic affiliation. The primer sequence is fluorescently labeled and it is close to the 5' end of the 16S rDNA gene. 'Gap' is the missing part of the sequence between the position of the primer and the beginning of the sequence. The position of the target sequence determines the size of the terminal fragment.