iTriplet, a rule-based nucleic acid sequence motif finder |
| |
Authors: | Eric S Ho Christopher D Jakubowski Samuel I Gunderson |
| |
Affiliation: | (1) Department of Molecular Biology and Biochemistry, Nelson Laboratories, Rutgers University, Room A322, 604 Allison Rd, Piscataway, NJ 08854, USA |
| |
Abstract: | Background With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|