Combinatorial algorithms for dna sequence assembly pdf

The sequence reconstruction problem that we take as our formulation of dna sequence assembly is a variation. Combinatorial algorithms for dna sequence assembly john d. Citeseerx combinatorial algorithms for dna sequence assembly. 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. 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. 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. Graphbased sequence assembly models represent sequence reads and their inferred relationships to one another as vertices and edges in the graph. Citeseerx document details isaac councill, lee giles, pradeep teregowda. 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 f a. 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. 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. The theory and practice of genome sequence assembly.

This assembly process, described in more detail below and. Pdf combinatorial algorithms for dna sequence assembly. Combinatorial algorithms for dna sequence 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. Combinatorial 3d shape generation via sequential assembly.