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Rough positioning of the primer binding sites

At first the rough melting characteristic of the exon must be visualized. Therefore the primers should be moved into the flanking intronic regions of the exon, so that they encompass the exon and the splice site. Primer dimers do not matter in this step. The melting characteristics are calculated and displayed on pressing ``m''. The program then asks which primer a clamp should be attached to. In the beginning it is useful to chose ``TRY ALL''. Melting profiles for all four variants are the result: no clamp at all, clamped forward primer, clamped reverse primer and bipolar clamping (i. e. both primers are clamped). One of the three clamped versions must be chosen according to the melting behavior. The interpretation of melting profiles is explained in the README of MELT87 which can be viewed via the help menu. In some cases the fragment needs to be split into smaller overlapping parts.




2001-12-04