Scoring Pairwise Genomic Sequence Alignments

@article{Chiaromonte2001ScoringPG,
  title={Scoring Pairwise Genomic Sequence Alignments},
  author={Francesca Chiaromonte and V. B. Yap and William Miller},
  journal={Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
  year={2001},
  pages={
          115-26
        }
}
The parameters by which alignments are scored can strongly affect sensitivity and specificity of alignment procedures. While appropriate parameter choices are well understood for protein alignments, much less is known for genomic DNA sequences. We describe a straightforward approach to scoring nucleotide substitutions in genomic sequence alignments, especially human-mouse comparisons. Scores are obtained from relative frequencies of aligned nucleotides observed in alignments of non-coding, non… CONTINUE READING

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