TAILIEUCHUNG - Báo cáo sinh học: "iTriplet, a rule-based nucleic acid sequence motif finder"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: iTriplet, a rule-based nucleic acid sequence motif finder. | Algorithms for Molecular Biology BioMed Central Research iTriplet a rule-based nucleic acid sequence motif finder Eric S Ho Christopher D Jakubowski and Samuel I Gunderson Open Access Address Rutgers University Department of Molecular Biology and Biochemistry Nelson Laboratories Room A322 604 Allison Rd Piscataway NJ 08854 uSa Email Eric S Ho - ericho@ Christopher D Jakubowski - chrisjak@ Samuel I Gunderson - gunderson@ Corresponding author Published 29 October 2009 Received 7 May 2009 Algorithms for Molecular Biology 2009 4 14 doi 1748-7188-4-14 Accepted 29 October 2009 This article is available from http content 4 1 14 2009 Ho et al licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 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. Results We have conducted a comprehensive assessment on the performance and sensitivityspecificity of

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