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, GenAl (Genomic Alignment), was developed that implements the algorithm. Its use is demonstrated on two retroviruses.
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Correspondence to: J. Hein
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Hein, J., Støvlæk, J. Genomic alignment. J Mol Evol 38, 310–316 (1994). https://doi.org/10.1007/BF00176094
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DOI: https://doi.org/10.1007/BF00176094