Name
Abstract | ||
|---|---|---|
Exact match queries, wildcard match queries, and k-mismatch queries are widely used in lots of molecular biology applications including the searching of ESTs (Expressed Sequence Tag) and DNA transcription factors. In this paper, we suggest an efficient indexing and processing mechanism for such queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as the R*-tree. Also, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in indexing space. Our query processing method converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1007/11430919_21 | PAKDD |
Keywords | Field | DocType |
genetic alphabet,k-mismatch query,indexing method,multi-dimensional index,position information,dna index structure,processing mechanism,dna transcription factor,dna sequence,multi-dimensional rectangle,efficient indexing,exact match query,indexing space,expressed sequence tag,nucleotides,molecular biology,indexing,sliding window,genetics,transcription factor,indexation | R-tree,Data mining,Wildcard,Expressed sequence tag,Sliding window protocol,DNA database,Computer science,Rectangle,Search engine indexing,Algorithm,Knowledge extraction | Conference |
Volume | ISSN | ISBN |
3518 | 0302-9743 | 3-540-26076-5 |
Citations | PageRank | References |
0 | 0.34 | 7 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Woo-Cheol Kim | 1 | 37 | 5.46 |
| Sanghyun Park | 2 | 729 | 80.64 |
| Jung-Im Won | 3 | 86 | 10.56 |
| Sang-Wook Kim | 4 | 792 | 152.77 |
| Jee-Hee Yoon | 5 | 49 | 8.70 |