Pattern search in Database Sequences
Search strings of the form (eg. fingerprint MCP-2, Bfa I, Hinf I, Rsa I, Dpn I, Dde I, Alu I) CTAGN177–181GANTCN90–94GTACN3–7GATCN41–45CTNAGN123–127AGCT were derived from the restriction fingerprints. The distances between the restriction sites were set to be flexible (+/-2 bp of the empirical length), because the experimentally analyzed fragment lengths have non-integer numbers and do not correspond to sequence length in base pairs better than +/-1 bp. The strings served as an input to the Perl script prosite_scan (author: Kay Hofmann ) searching the nucleotide section of GenBank (downloaded April 12th 2000).