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Online Journal of Bioinformatics


Volume 6 (2) 162-173, 2005.

The Effect of Inverse Document Frequency Weights on DNA Sequence Retrieval


O'Kane KC


Department of Computer Science, The University of Northern Iowa, Cedar Falls, Iowa 50613-0507, USA.




O'Kane KC, The Effect of Inverse Document Frequency Weights on DNA Sequence Retrieval, Onl J Bioinform., 6 (2):162-173, 2005. This paper presents a method to identify weighted n-gram sequence fragments in large genomic databases whose indexing characteristics permits the construction of fast, indexed, sequence retrieval programs where query processing time is determined mainly by the size of the query and number of sequences retrieved rather than, as is the case in sequential scan based systems such as BLAST, FASTA, and Smith-Waterman, the size of the database.  The weighting scheme is based on the inverse document frequency (IDF) method, a weighting formula that calculates the relative importance of indexing terms based on term distribution.  In the experiments, the relative IDF weights of all segmented, overlapping, fixed n-grams of length eleven in the NCBI nt and other databases were calculated and the resulting n-grams ranked and used to create an inverted index into the sequence file.  The system was evaluated on test cases constructed from randomly selected known sequences which were randomly fragmented and mutated and the results compared with BLAST and MegaBlast for accuracy and speed.  Due to the speed of query processing, the system is also capable of database sequence clustering, examples of which are given


KEY WORDS: inverse document frequency; sequence retrieval; sequence clustering; n-grams; inverted index.