Wang X, Wang S, Song T. A Spectral Rotation Method with Triplet Periodicity Property for Planted Motif Finding Problems.
Comb Chem High Throughput Screen 2019;
22:683-693. [PMID:
31782356 DOI:
10.2174/1386207322666191129112433]
[Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND
Genes are known as functional patterns in the genome and are presumed to have biological significance. They can indicate binding sites for transcription factors and they encode certain proteins. Finding genes from biological sequences is a major task in computational biology for unraveling the mechanisms of gene expression.
OBJECTIVE
Planted motif finding problems are a class of mathematical models abstracted from the process of detecting genes from genome, in which a specific gene with a number of mutations is planted into a randomly generated background sequence, and then gene finding algorithms can be tested to check if the planted gene can be found in feasible time.
METHODS
In this work, a spectral rotation method based on triplet periodicity property is proposed to solve planted motif finding problems.
RESULTS
The proposed method gives significant tolerance of base mutations in genes. Specifically, genes having a number of substitutions can be detected from randomly generated background sequences. Experimental results on genomic data set from Saccharomyces cerevisiae reveal that genes can be visually distinguished. It is proposed that genes with about 50% mutations can be detected from randomly generated background sequences.
CONCLUSION
It is found that with about 5 insertions or deletions, this method fails in finding the planted genes. For a particular case, if the deletion of bases is located at the beginning of the gene, that is, bases are not randomly deleted, then the tolerance of the method for base deletion is increased.
Collapse