is only moved if overlap is a small fraction of A or else B is rejected. In the above case, both A and B can be moved. We first move the start of B until the overlap region scores higher for B. Then we move the start of A until it scores higher. Then B again, and so on, until either the overlap is eliminated or no further moves can be made. The above example has been taken from the paper 'Identifying bacterial genes and endosymbiont DNA with Glimmer''Ribosome binding sites Ribosome binding site(RBS) signal can be used to find true start site position. GLIMMER results are passed as an input for RBSfinder program to predict ribosome binding sites. GLIMMER 3.0 integrates RBSfinder program into gene predicting function itself. ELPH software( which was determined as highly effective at identifying RBS in the paper) is used for identifying RBS and is available at this website. Gibbs sampling algorithm is used to identify shared motif in any set of sequences. This shared motif sequences and their length is given as input to ELPH. ELPH then computes the position weight matrix(PWM) which will be used by GLIMMER 3 to score any potential RBS found by RBSfinder. The above process is done when we have a substantial amount of training genes. If there are inadequate number of training genes, GLIMMER 3 can bootstrap itself to generate a set of gene predictions which can be used as input to ELPH. ELPH now computes PWM and this PWM can be again used on the same set of genes to get more accurate results for start-sites. This process can be repeated for many iterations to obtain more consistent PWM and gene prediction results. Performance Glimmer supports genome annotation efforts on a wide range of bacterial, archaeal, and viral species. In a large-scale reannotation effort at the DNA Data Bank of Japan (DDBJ, which mirrors Genbank). Kosuge et al.'' (2006) examined the gene finding methods used for 183 genomes. They reported that of these projects, Glimmer was the gene finder for 49%, followed by GeneMark with 12%, with other algorithms used in 3% or fewer of the projects. (They also reported that 33% of genomes used "other" programs, which in many cases meant that they could not identify the method. Excluding those cases, Glimmer was used for 73% of the genomes for which the methods could be unambiguously