What is it about?
Our study aims to answer the question: Is it possible to map massive eukaryotic DNA content into numbers and use them for effective search of key DNA patterns, such as: promoter consensus sequence, TSS, PolyA signal,...etc.
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Why is it important?
- Provides more precise DNA matching analysis. - New formula for fast indexing of massive eukaryotic DNA content. - Storage aspects improved by dynamic construction of the indexed data structure. - Fast pattern searching/recognition due to the use of Sorted Dictionary instead of Hash Table. - All patterns are identified, regardless of their starting positions in the indexed samples.
Perspectives
The biological impact of the proposed methodology lies in the ability to detect all DNA pattern hits, regardless of their starting positions in the sequences. Unlike SSAHA and the approach of Renker and Shyu, our algorithm can identify DNA pattern hits which are located at the beginnings of the indexed DNA sequences, by integrating suffix search and prefix search. As a consequence, the algorithm proposed by us is expected to provide more precise matching in DNA pattern analyses by being able to identify key DNA pattern hits that might indicate functional DNA data unreported by SSAHA and Reneker and Shyu's method.
Ph.D Done Stojanov
Univerzitet Goce Delcev Stip
Read the Original
This page is a summary of: Towards computational improvement of DNA database indexing and short DNA query searching, Biotechnology & Biotechnological Equipment, September 2014, Taylor & Francis,
DOI: 10.1080/13102818.2014.959711.
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