Sequence alignment with tandem duplication
- Mount Sinai School of Medicine, New York, NY (United States)
Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 548993
- Report Number(s):
- CONF-970137-; TRN: 97:005298-0005
- Resource Relation:
- Conference: RECOMB `97: 1. annual conference on research in computational molecular biology, Santa Fe, NM (United States), 20-22 Jan 1997; Other Information: PBD: 1997; Related Information: Is Part Of RECOMB 97. Proceedings of the first annual international conference on computational molecular biology; PB: 370 p.
- Country of Publication:
- United States
- Language:
- English
Similar Records
Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome
Sequence duplication and internal deletion in the integrated human papillomavirus type 16 genome cloned from a cervical carcinoma
Related Subjects
BASIC STUDIES
99 MATHEMATICS
COMPUTERS
INFORMATION SCIENCE
MANAGEMENT
LAW
MISCELLANEOUS
HEREDITARY DISEASES
ETIOLOGY
DNA
DNA SEQUENCING
MUTATIONS
HUMAN POPULATIONS
GENOME MUTATIONS
GENES
STRUCTURE-ACTIVITY RELATIONSHIPS
GENE REGULATION
BIOLOGICAL EVOLUTION
GENE MUTATIONS
GENETIC MAPPING
ALGORITHMS
COMPUTER CODES
MOLECULAR BIOLOGY
NUCLEOTIDES
INTRONS