PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.

@article{Birney1996PairWiseAS,
  title={PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.},
  author={Ewan Birney and James D. Thompson and Toby J. Gibson},
  journal={Nucleic acids research},
  year={1996},
  volume={24 14},
  pages={2730-9}
}
DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments. A dynamic… CONTINUE READING

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