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sn output a string s that contains all strings s1

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Unformatted text preview: lies genes duplicate & then diverge •  Segmental duplicaCons ~very long, very similar copies Fragment Assembly •  ComputaConal Challenge: assemble individual short fragments (reads) into a single genomic sequence (“superstring”) •  UnCl late 1990s the shotgun fragment assembly of human genome was viewed as intractable problem Shortest Superstring Problem •  Problem: Given a set of strings, find a shortest string that contains all of them •  Input: Strings s1, s2,…., sn •  Output: A string s that contains all strings s1, s2,…., sn as substrings, such that the length of s is minimized •  Complexity: NP- complete •  Note: this formulaCon does not take into account sequencing errors Algorithms for Fragment Assembly Whole Genome Shotgun Sequencing Genome Genome amplified and sliced into smaller fragments (>=600bp) Build consensus sequence from overlap Overlap- Layout- Consensus Assemblers: ARACHNE, PHRAP, CAP, TIGR, CELERA Overlap: find potenCally overlapping reads Layout: merge reads into conCgs and conCgs into superconCgs Consensus: derive the DNA sequence and correct read errors ..ACGATTACAATAGGTT.. Overlap •  Eread is compared to that of every other read, in both the forward and reverse complement orientaCons. •  As such, the overlap computaCon step is a very Cme intensive step – especially if the set of reads is very large. •  For example, the whole genome shotgun assembly of Drosophila had about 3 x 10^6 reads of 500 bases, requiring roughly 10^13 comparisons (Deonier et al., 2010). •  Even on today's...
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