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COMIT: identification of noncoding motifs under selection in coding sequences.

Kural D, Ding Y, Wu J, Korpi AM, Chuang JH - Genome Biol. (2009)

Bottom Line: Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences.COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs.Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA. kural@bc.edu

ABSTRACT
Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

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Comparison of COMIT z-scores to maximum likelihood Ks scores. There is a clear correlation between mouse-human z-scores and mouse-human Ks based on (a) naïve codon completion or (b) nucleotide-by-nucleotide Ks. These correlations indicate that the qualitative conservation of many motifs is not method-dependent.
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Figure 3: Comparison of COMIT z-scores to maximum likelihood Ks scores. There is a clear correlation between mouse-human z-scores and mouse-human Ks based on (a) naïve codon completion or (b) nucleotide-by-nucleotide Ks. These correlations indicate that the qualitative conservation of many motifs is not method-dependent.

Mentions: We first compared the motif z-scores to the Ks values from the naïve codon completion method. Figure 3a shows the Ks values for each motif calculated from human-mouse alignments compared to the z-score values for each motif for human-mouse. We observed a clear correlation between the z-scores and Ks.


COMIT: identification of noncoding motifs under selection in coding sequences.

Kural D, Ding Y, Wu J, Korpi AM, Chuang JH - Genome Biol. (2009)

Comparison of COMIT z-scores to maximum likelihood Ks scores. There is a clear correlation between mouse-human z-scores and mouse-human Ks based on (a) naïve codon completion or (b) nucleotide-by-nucleotide Ks. These correlations indicate that the qualitative conservation of many motifs is not method-dependent.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091326&req=5

Figure 3: Comparison of COMIT z-scores to maximum likelihood Ks scores. There is a clear correlation between mouse-human z-scores and mouse-human Ks based on (a) naïve codon completion or (b) nucleotide-by-nucleotide Ks. These correlations indicate that the qualitative conservation of many motifs is not method-dependent.
Mentions: We first compared the motif z-scores to the Ks values from the naïve codon completion method. Figure 3a shows the Ks values for each motif calculated from human-mouse alignments compared to the z-score values for each motif for human-mouse. We observed a clear correlation between the z-scores and Ks.

Bottom Line: Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences.COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs.Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA. kural@bc.edu

ABSTRACT
Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

Show MeSH