PcrBase : un logiciel d'aide à la PCR en interface avec les banques d'acides nucléiques.

Abstract

PCR, polymerase chain reaction, is a powerful technique of nucleic sequence amplification. It requires to choose two oligonucleotides at each extremity of the segment to be amplified. These oligonucleotides must be carefully chosen according to specific rules that are necessary for an optimal yield of amplification. PcrBase is a software designed to select one or more oligonucleotide couples for the amplification of personal sequences or database sequences (EMBL, GenBank). With PcrBase, the user has the possibility to search oligonucleotides according to the following criteria: (i) the upstream and downstream limits of the region to amplify as well as the range of search from both sides of this area, (ii) the oligonucleotide size and their C+C percentage, (iii) the occurrence or not of GC dinucleotide succession at the 3' end, (iv) the maximum number of consecutive matched bases susceptible to make hairpins in the oligonucleotide, (v) the maximum number of consecutive matched bases that ma)l appear in tile dimer made by the two oligonucleotides. Once the selection criteria have been established, the software will test the specificity of oligonucleotides on the whole set of sequences of GenBank.