Aligning a DNA sequence with a protein sequence.
We develop several algorithms for the problem of aligning DNA sequence with a protein sequence. Our methods account for frameshift errors, but not for introns in the DNA sequence. Thus, they are particularly appropriate for comparing a cDNA sequence that suffers from sequencing errors with an amino acid sequence or a protein sequence database. We describe algorithms for computing optimal alignments for several definitions of DNA-protein alignment, verify sufficient conditions for equivalence of certain definitions, describe techniques for efficient implementation, and discuss experience with these ideas in a new release of the FASTA suite of database-searching programs.
Zhang
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Department of Computer Science and Engineering, The Pennsylvania State University, University Park 16802, USA. zzhang@galapagos.cse.psu.edu
Pearson
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Miller
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D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D016208:Databases, Factual; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
D011506:Proteins; D004247:DNA