A new DNA alignment method based on inverted index
Wang Liang, Zhao KaiYong
(Submitted on 30 Jun 2013)
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is still not found. This paper just discuss such applications. Three main problems, DNA segmenting, long DNA query search, DNA search ranking algorithm and evaluation method are detailed respectively. This research presents a new avenue to build more effective DNA alignment methods.
Haldane's Sieve 
Inverted index and gram-based search algorithms for short DNA sequences already exist.
See the introduction of the Hobbes paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315303/) for a survey.