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Pattern matching plays a central role in different§aspects of biological sequence analysis, and has been§used in applications as diverse as short-gun§sequencing, multiple sequence alignments, gene§finding, analysis of repetition structures, searching§for unique oligonucleotides, prediction of protein§function and structure, sequence homology search,§finding DNA-binding protein motifs, etc. Suffix trees§and suffix arrays are primary data structures used in§rapid pattern matching. And the problem of suffix§sorting is a fundamental problem in constructing§suffix arrays. This book presents the basics,§concepts of suffix trees, suffix arrays and suffix§sorting and proposes a direct suffix sorting§algorithm which rearranges the biological sequences§of interests and facilitate high throughput pattern§query, retrieval and storage in linear time. The§direct suffix sorting algorithm is then applied to§solve practical problems in multiple sequence§alignment and data compression. The book serves both§as reference for computer scientists, computational§biologists and bio-informatic professionals and an§essential study materials for graduate and advanced§courses on computational biology.
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