DocumentCode :
22373
Title :
Approximate 
-Mer Matching Using Fuzzy Hash Maps
Author :
Healy, John ; Chambers, David H.
Author_Institution :
Dept. of Comput. & Math., Galway-Mayo Inst. of Technol., Galway, Ireland
Volume :
11
Issue :
1
fYear :
2014
fDate :
Jan.-Feb. 2014
Firstpage :
258
Lastpage :
264
Abstract :
We present a fuzzy technique for approximate k-mer matching that combines the speed of hashing with the sensitivity of dynamic programming. Our approach exploits the collision detection mechanism used by hash maps, unifying the two phases of “seed and extend” into a single operation that executes in close to O(1) average time.
Keywords :
bioinformatics; dynamic programming; fuzzy set theory; approximate k-Mer matching; collision detection; dynamic programming; fuzzy hash maps; fuzzy technique; single operation; Bioinformatics; Computational biology; Genomics; Heuristic algorithms; Indexes; Prototypes; Sensitivity; Biology and genetics; fuzzy set;
fLanguage :
English
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
Publisher :
ieee
ISSN :
1545-5963
Type :
jour
DOI :
10.1109/TCBB.2014.2309609
Filename :
6758383
Link To Document :
