DNA sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. Genomic sequences frequently contain repeat elements that may confound the fragment assembly process, and errors in fragment assembly, and errors in fragment assembly may seriously impact the biological interpretation of the sequence data. Validating the fidelity of sequence assembly by experimental means is desirable. This report examines the use of restriction digest analysis as a method for testing the fidelity of sequence assembly. Restriction digest fingerprint matching is an established technology for high resolution physical map construction, but the requirements for assembly validation differ from those of fingerprint mapping. Fingerprint matching is a statistical process that is robust to the presence of errors in the data and independent of absolute fragment mass determination. Assembly validation depends on the recognition of a small number of discrepant fragments and is very sensitive to both false positive and false negative errors in the data. Assembly validation relies on the comparison of absolute masses derived from sequence with masses that are experimenally determined, making absolute accuracy as well as experimental precision important. As the size of a sequencing project increases, the difficulties in assembly validation by restriction fingerprinting befcome more severe. Simulation studies are used to demonstrate that large-scale errors in sequence assembly can escape detection in fingerprint pattern comparison. Alternative technologies for sequence assembly validation are discussed
