Paper Info
Title
Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing
Abstract
In the past, genome sequence databases had used main memory indexing, such as the suffix tree, for fast sequence searches. With next generation sequencing technologies, the amount of sequence data being generated is huge and main memory indexing is limited by the amount of memory available. K-mer based techniques are being more used for various genome sequence database applications such as local alignment. K-mer can also provide an excellent basis for creating efficient disk based indexing. In this paper, we have proposed a k-mer based database searching and local alignment tool using box queries on BoND-SD-tree indexing. BoND-tree is quite efficient for indexing and searching in Non-Ordered Discrete Data Space (NDDS). We have conducted experiments on searching DNA sequence databases using back translated protein query sequences and have compared with existing methods. We have also implemented local alignment of back translated protein query sequences with large DNA sequence databases using this index based k-mer search. Performances of this local alignment approach has been compared with that of Tblastn of NCBI. The results are quite promising and justify significance of the proposed approach.
Year
DOI
Venue
2015
10.1109/BIBE.2015.7367638
IEEE International Conference on Bioinformatics and Bioengineering
Keywords
DocType
Citations 
NCBI Tblastn,index based k-mer search,back translated protein query sequences,NonOrdered Discrete Data Space,box queries,disk based indexing,K-mer based techniques,fast sequence search,suffix tree,main memory indexing,genome sequence database,BoND-SD-tree indexing,DNA sequence database,local alignment,back translated peptide K-mer search
Conference
1
PageRank 
References 
Authors
0.35
4
5
Name
Order
Citations
PageRank
A. K. M. Tauhidul Islam111.03
Sakti Pramanik2770204.19
Xinge Ji310.35
J R Cole433169.86
Qiang Zhu539860.85