Combinatorial algorithms for dna sequence assembly 1 j. Combinatorial algorithms for dna sequence assembly 1 introduction dna sequences may be viewed abstractly as strings over the four letter alphabet. Theoretical studies on combinatorial solutions to the sequence assembly problem led to the development of practical software using graphbased representations of the sequence data 45, 68. Replace 1 a 1 combinatorial algorithms for dna sequence processing bhaskar dasgupta department of computer science university of illinois at chicago chicago, il 60607 email. Genetic algorithms and dna sequence assembly the laboratory processes for dna sequencing are still limited to relatively short stretches of dna, necessitating the assembly of longer sequences based on the base configuration of the shorter sequences. The trend toward very large dna sequencing projects, such as those being undertaken as part of the human genome program, necessitates the development of efficient and precise algorithms. Pdf combinatorial algorithms for dna sequence assembly. Combinatorial algorithms for dna sequence assembly 1 introduction dna sequences may be viewed abstractly as strings over the four letter alphabet f a.
Citeseerx document details isaac councill, lee giles, pradeep teregowda. The trend towards very large dna sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long dna sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of dna sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing. Combinatorial algorithms for dna sequence assembly john d. The theory and practice of genome sequence assembly. The sequence reconstruction problem that we take as our formulation of dna sequence assembly is a variation. N2 the trend toward very large dna sequencing projects, such as those being undertaken as part of the human genome program, necessitates the development of efficient and precise algorithms for assembling a long dna sequence from the fragments obtained by. Combinatorial 3d shape generation via sequential assembly. The trend toward very large dna sequencing projects, such as those being undertaken as part of the human genome program, necessitates the development of efficient and precise algorithms for assembling a long dna sequence from the fragments obtained by shotgun sequencing or other methods.