title: Genomic alignment.
abstract: As sequencing techniques become increasingly efficient, the average length of a sequence is bound to grow. Traditional sequence-comparison algorithms can either compare DNA or protein, but not a mixture, which is actually a common situation. Most obtained DNA sequences contain coding regions, and it is more reliable to compare the coding regions as protein than just as DNA. A heuristic algorithm is presented that can compare DNA with both coding and noncoding regions, but that also can compare multiple reading frames and determine which exons are homologous. A program, GenA1 (Genomic Alignment), was developed that implements the algorithm. Its use is demonstrated on two retroviruses.
authors.affiliation: Institute of Biological Sciences, Aarhus University, Denmark.
authors.forename: J
authors.initials: J
authors.lastname: Hein
authors.forename: J
authors.initials: J
authors.lastname: Støvlbaek
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics; D015750:Genes, gag; D015751:Genes, pol; D015497:HIV-1 / Q000235:genetics; D015498:HIV-2 / Q000235:genetics; D008969:Molecular Sequence Data; D016364:Reading Frames; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D004279:DNA, Viral