A method for detecting a specific sequence, a mutation and/or a polymorphisms, including a single nucleotide polymorphism (SNP), is based on the use of RecA-like recombinase protein and primer extension (PE) or oligonucleotide ligation assays (OLA). RecA coated, specific DNA oligonucleotide probes (RecA filaments) are used for homology searching in duplex DNA. Location of homologous sequences results in the formation of D-loop or double D-loop structures containing a duplex regions comprising the oligonucleotide probe and one strand of the target DNA. In the case of the PE methods, probes are selected to terminate with their 3' end adjacent to the site of mutation or SNP such that a single nucleotide or terminator addition to the primer will be diagnostic of the mutation or SNP. In the case of the OLA methods, sets of oligonucleotide probes (ligation partners) are selected to have adjacent ends terminate at, or adjacent to, the site of mutation or SNP such that ligation is possible only when both ends are correctly base-paired. Successful ligation is diagnostic of the specific sequence, mutation or SNP. Also disclosed are compositions and kits useful for practicing the foregoing methods.