Βασίλης Πολυχρονόπουλος
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Τεχνικές κατασκευής δένδρων επιθεμάτων πολύ μεγάλου μεγέθους και χρήσης τους για γρήγορη αναζήτηση βιολογικών δεδομένων. Βασίλης Πολυχρονόπουλος. Βιολογικά Δεδομένα και Ακολουθίες. Το DNA περιέχει όλη τη γενετική πληροφορία ενός οργανισμού. - PowerPoint PPT Presentation
Transcript of Βασίλης Πολυχρονόπουλος
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DNA . . RNA . . .
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, . : (suffix trees) (suffix arrays)
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. ( ). / . 00
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. TRELLIS.
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trie
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[01] . . , . bin-packing . .
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DynaCluster [CYH05] TOP-Q[BH04]DynaCluster TOP-Q ,
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TDD [THP04] Hunt. wotdeager . wotdeager: uffering cache .
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TRELLIS [PZ07]
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&
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TRELLIS trie LCA : LCA LCE
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C++. ( NCBI): . . . .
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: query. data.: .Knuth-Morris-PrattBoyer-Moore
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( query)
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( )
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: query. data.: . .
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( query)
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( )
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:query 40 bytes k=3: ( + ). cut-off heuristic.
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(Mbps)Ukkonen 85 (sec) (sec)10,33820,64851,5103103,0198
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: 8 : brute-force .
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(1) Boyer-Moore, , query dataset dataset query
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(2) / LCE LCE
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TRELLIS DNA TRELLIS (27 bytes/) LCE ( , )
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[BH04] Bedathur S., Haritsa J., Engineering a fast online persistent suffix tree construction, 20th International Conference on Data Engineering, 2004.[CYL05] Cheung C., Yu J., Lu H., Constructing suffix tree for gigabyte sequences with megabyte memory, IEEE Transactions on Knowledge and Data Engineering, 17(1):90105, 2005.[HAI01] Hunt E., Atkinson ., Irving R., A database index to large biological sequences, 27th International Conference on Very Large Data Bases, 2001.[PZ07] Phophakdee B., Zaki M., Genome-scale Disk-based Suffix Tree Indexing, ACM SIGMOD International Conference on Management of Data, 2007.[THP04] Tata S., Hankins R., Patel J., Practical suffix tree construction, 30th International Conference on VLDB, 2004.
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..;
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(nm) n X m (n+m) LCE (kn) k , (mn)
