Aligning a DNA sequence with a protein sequence

Conference · Sun Nov 30 23:00:00 EST 1997

OSTI ID:549033

Zhang, Zheng; Miller, W ^[1]; Pearson, W R ^[2]

---

1. Pennsylvania State Univ., University Park, PA (United States)
2. Univ. of Virginia, Charlottesville, VA (United States)

We develop several algorithms for the problem of aligning a 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 contains sequencing errors with an amino acid sequence or a protein sequence database. We describe techniques for efficient implementation, verify sufficient conditions for equivalence of several definitions of alignments, and discuss experience with these ideas in a new release of the fasta suite of database-searching programs. 10 refs., 8 figs.

• Research Organization: Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
• OSTI ID: 549033
• Report Number(s): CONF-970137--
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
AMINO ACID SEQUENCE
AMINO ACIDS
CORRELATIONS
DATA BASE MANAGEMENT
DNA
DNA SEQUENCING
DYNAMIC PROGRAMMING
EFFICIENCY
ERRORS
F CODES
GENETIC MAPPING
INTRONS
MATHEMATICAL MODELS
MOLECULAR BIOLOGY
NUCLEOTIDES
PROTEINS
STRUCTURE-ACTIVITY RELATIONSHIPS