CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.

BMC Bioinformatics
Yang DingJeffrey H Chuang

Abstract

It has been increasingly appreciated that coding sequences harbor regulatory sequence motifs in addition to encoding for protein. These sequence motifs are expected to be overrepresented in nucleotide sequences bound by a common protein or small RNA. However, detecting overrepresented motifs has been difficult because of interference by constraints at the protein level. Sampling-based approaches to solve this problem based on codon-shuffling have been limited to exploring only an infinitesimal fraction of the sequence space and by their use of parametric approximations. We present a novel O(N(log N)2)-time algorithm, CodingMotif, to identify nucleotide-level motifs of unusual copy number in protein-coding regions. Using a new dynamic programming algorithm we are able to exhaustively calculate the distribution of the number of occurrences of a motif over all possible coding sequences that encode the same amino acid sequence, given a background model for codon usage and dinucleotide biases. Our method takes advantage of the sparseness of loci where a given motif can occur, greatly speeding up the required convolution calculations. Knowledge of the distribution allows one to assess the exact non-parametric p-value of whether a giv...Continue Reading

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Citations

Dec 4, 2012·Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment·C A ElkinsI R Patel
Mar 26, 2016·Frontiers in Microbiology·Patrick SobetzkoTorsten Waldminghaus
Feb 21, 2018·BMC Developmental Biology·Anna MantsokiAnagha Joshi
Jan 24, 2019·Frontiers in Genetics·Yu-Ting ChenYen-Wei Chu

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Methods Mentioned

BETA
immunoprecipitation
ChIP-seq

Software Mentioned

MEME
Python
PERL
Ensembl
CodingMotif
GABP
GALAXY
scripts

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