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Efficient computer programs have made it possible to elucidate and analyze large-scale genomic sequences. Fundamental tasks, such as the assembly of numerous whole-genome shotgun fragments, the alignment of complementary DNA sequences with a long genome, and the design of gene-specific primers or oligomers, require efficient algorithms and state-of-the-art implementation techniques. This textbook emphasizes basic software implementation techniques for processing large-scale genome sequences and provides executable sample programs.
Sample Chapter(s)
Chapter 1: Simple String Search (407 KB)
Contents:
- Simple String Search
- Sorting
- Lookup Tables
- Suffix Arrays
- Space-Efficient String Search
- Approximate String Search
- Seeded Alignments
- Whole Genome Shotgun Sequencing
Readership: Course textbook for advanced undergraduate students in computer science and biology; biotechnology and computer industry and non-experts interested in advanced genome processing algorithms.
