:: DESCRIPTION
CodingMotif calculates the exact motif P value under a Markov model that preserves the dinucleotide frequency as well as codon usage.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.
Ding Y, Lorenz WA, Chuang JH.
BMC Bioinformatics. 2012 Feb 14;13:32. doi: 10.1186/1471-2105-13-32.
:: DESCRIPTION
freqAnalysis was designed to identify statistically aberrant k-length nucleotide motifs in coding DNA sequences, specifically to identify putative programmed translational frameshift sites. These are short sequences capable of inducing highly efficient ribosomal frameshifting by destabilizing normal ribosome-mRNA interaction. Because of the potentially catastrophic effect of frameshifting on normal protein production, we reasoned, such sites would be selected against by evolution and hence statistically underrepresented in protein-encoding sequences.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2002 Aug;18(8):1046-53.
Computational identification of putative programmed translational frameshift sites.
Shah AA, Giddings MC, Parvaz JB, Gesteland RF, Atkins JF, Ivanov IP.
