Loading...
Please wait, while we are loading the content...
Similar Documents
Good spaced seeds for homology search (2004)
| Content Provider | CiteSeerX |
|---|---|
| Author | Choi, Kwok Pui Zeng, Fanfan Zhang, Louxin |
| Abstract | Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. Results: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences. Contact: |
| File Format | |
| Volume Number | 20 |
| Journal | BIOINFORMATICS |
| Language | English |
| Publisher Date | 2004-01-01 |
| Access Restriction | Open |
| Subject Keyword | Homology Search Spaced Seed Local Alignment Dna Genomic Sequence Contiguous Position Match Pattern Matching Position Similarity Level Patternhunter Program Numerical Computation Diverse Similarity Homologous Sequence Blast Program Certain Pattern Sequence Similarity Good Spaced Seed Important Technique |
| Content Type | Text |
| Resource Type | Article |
