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PubMed · 8006999

Genomic alignment.

J Hein·J Støvlbaek
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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.

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AlgorithmsAmino Acid SequenceBase SequenceDNA, ViralGenes, gagGenes, polHIV-1HIV-2Molecular Sequence DataReading FramesSequence AlignmentSoftwareComparative StudyJournal ArticleResearch Support, Non-U.S. Gov't

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J Hein, J Støvlbaek. 1994. Genomic alignment.. https://doi.org/10.1007/bf00176094

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