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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.

Show MeSH
Conservation of hexamer submotifs of the yeast ACS DNA replication origin motif. Of the 24 hexamers, 21 are consistent with the ACS consensus TKTTTATRTTTWGTT and have positive z-scores in comparisons of S. cerevisiae and S. bayanus coding sequences. These results support the hypothesis that ACS motifs in coding regions are functionally active, and also indicate that COMIT is capable of detecting coding motifs functional at the DNA level.
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Figure 7: Conservation of hexamer submotifs of the yeast ACS DNA replication origin motif. Of the 24 hexamers, 21 are consistent with the ACS consensus TKTTTATRTTTWGTT and have positive z-scores in comparisons of S. cerevisiae and S. bayanus coding sequences. These results support the hypothesis that ACS motifs in coding regions are functionally active, and also indicate that COMIT is capable of detecting coding motifs functional at the DNA level.

Mentions: COMIT gives consistently positive scores for the ACS motif in coding regions. We tested the z-scores of all 6-mers that coincide with this motif, given the degenerate consensus TKTTTATRTTTWGT. We found that 21 of 24 6-mers have positive z-scores based on coding sequence alignments of S. cerevisiae and S. bayanus (Figure 7). These results support the hypothesis that ACS motifs in coding regions are functionally active and suggest that COMIT is capable of detecting coding motifs functional at the DNA level.


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

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

Conservation of hexamer submotifs of the yeast ACS DNA replication origin motif. Of the 24 hexamers, 21 are consistent with the ACS consensus TKTTTATRTTTWGTT and have positive z-scores in comparisons of S. cerevisiae and S. bayanus coding sequences. These results support the hypothesis that ACS motifs in coding regions are functionally active, and also indicate that COMIT is capable of detecting coding motifs functional at the DNA level.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Conservation of hexamer submotifs of the yeast ACS DNA replication origin motif. Of the 24 hexamers, 21 are consistent with the ACS consensus TKTTTATRTTTWGTT and have positive z-scores in comparisons of S. cerevisiae and S. bayanus coding sequences. These results support the hypothesis that ACS motifs in coding regions are functionally active, and also indicate that COMIT is capable of detecting coding motifs functional at the DNA level.
Mentions: COMIT gives consistently positive scores for the ACS motif in coding regions. We tested the z-scores of all 6-mers that coincide with this motif, given the degenerate consensus TKTTTATRTTTWGT. We found that 21 of 24 6-mers have positive z-scores based on coding sequence alignments of S. cerevisiae and S. bayanus (Figure 7). These results support the hypothesis that ACS motifs in coding regions are functionally active and suggest that COMIT is capable of detecting coding motifs functional at the DNA level.

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