This paper describes the unerlying mathematical model and the dynamic programming algorithm technique for the valicdation of a (DNA) sequence against a (DNA) map. The sequence can be obtained from a variety of sources (r,g, GenBAnk, Sanger's Lab, or Celera P.E.) and it is assumed to be written out as a string of nucleotides. The map is an ordered restriction map obtained through an optical mapping process and is augmented with statistical information which will ne used to place (or not) the sequence in the genome. Our approach has many other applications beyond validation: e.g. map-based sequence assembly, phasing sequence contigs, detecting and closing gaps and annotation of partially sequenced genomes to find open reading frames, genes and synteny groups. We tested our system by checking various maps against publicly available sequence data for Plasmodium falciparum.