title: Should nucleotide sequence analyzing computer algorithms always extend homologies by extending homologies?
abstract: Most computer algorithms used for comparing or aligning nucleotide sequences rely on the premise that the best way to extend a homology between the two sequences is to select a match rather than a mismatch. We have tested this assumption and found that it is not always valid.
mesh_terms: D001483:Base Sequence; D003201:Computers; D004279:DNA, Viral / Q000032:analysis; D013539:Simian virus 40 / Q000235:genetics; D012984:Software
chemical_list: D004279:DNA, Viral