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Title: Indexing DNA sequences using q-grams
Authors: Cao, X.
Li, S.C.
Tung, A.K.H. 
Issue Date: 2005
Citation: Cao, X.,Li, S.C.,Tung, A.K.H. (2005). Indexing DNA sequences using q-grams. Lecture Notes in Computer Science 3453 : 4-16. ScholarBank@NUS Repository.
Abstract: We have observed in recent years a growing interest in similarity search on large collections of biological sequences. Contributing to the interest, this paper presents a method for indexing the DNA sequences efficiently based on q-grams to facilitate similarity search in a DNA database and sidestep the need for linear scan of the entire database. Two level index - hash table and c-trees - are proposed based on the q-grams of DNA sequences. The proposed data structures allow the quick detection of sequences within a certain distance to the query sequence. Experimental results show that our method is efficient in detecting similarity regions in a DNA sequence database with high sensitivity. © Springer-Verlag Berlin Heidelberg 2005.
Source Title: Lecture Notes in Computer Science
ISSN: 03029743
Appears in Collections:Staff Publications

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