Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions

A program has been developed for the modelling of modifications in DNA ends, for the construction of ligated junctions, and for the analysis in these junctions of new restriction enzyme recognition sequences. This program allows the analysis of restriction enzyme specificities in ligated junctions of cohesive or blunt DNA ends. Cohesive ends are considered in their natural configuration or after modification by possible blunt-ending procedures. The program also allows the modelling of partial filling-in for 5'-single-stranded ends. This program has proven useful for the design of sequences with new restriction sites or to predict or confirm the sequence of junctions created by the ligation of modified ends.