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Seeder: discriminative seeding DNA motif discovery.

Fauteux F, Blanchette M, Strömvik MV - Bioinformatics (2008)

Bottom Line: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters.The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.

ABSTRACT

Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.

Results: We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown to perform equally or better than other motif discovery tools. The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.

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Arabidopsis seed-specific motifs. Sequence logos of motifs overrepresented in the promoters of A. thaliana seed-specific marker genes. (A) Full-length forward motifs. (B) Reverse complement of motifs.
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Figure 3: Arabidopsis seed-specific motifs. Sequence logos of motifs overrepresented in the promoters of A. thaliana seed-specific marker genes. (A) Full-length forward motifs. (B) Reverse complement of motifs.

Mentions: The top two predictions (q-value <0.01) were compared to known plant motifs in the PLACE database (Higo et al., 1998) using the STAMP web server (Mahony and Benos, 2007). The first motif (Fig. 3, m1) (q-value=4.4 × 10−9, information content=7.4) and the second motif (Fig. 3, m2) (q-value=1.1 × 10−3, information content=7.6) are similar to two experimentally characterized cis-regulatory elements found in the napA promoter in B. napus, the RY repeat (CATGCA) (E=6.32 × 10−8) and the G-box (CACGTG) (E=2.92 × 10−5) (Ezcurra et al., 1999). The function of these regulatory elements was shown by substitution mutation analysis using promoter–reporter gene fusions, leading to a strong reduction of the napA promoter activity in seeds (Ezcurra et al., 1999). The second motif is also highly similar to a sequence (ACGTGTC) (E=4.70 × 10−11) overrepresented in the promoters of A. thaliana genes downregulated during seed germination (Ogawa et al., 2003).Fig. 3.


Seeder: discriminative seeding DNA motif discovery.

Fauteux F, Blanchette M, Strömvik MV - Bioinformatics (2008)

Arabidopsis seed-specific motifs. Sequence logos of motifs overrepresented in the promoters of A. thaliana seed-specific marker genes. (A) Full-length forward motifs. (B) Reverse complement of motifs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2562012&req=5

Figure 3: Arabidopsis seed-specific motifs. Sequence logos of motifs overrepresented in the promoters of A. thaliana seed-specific marker genes. (A) Full-length forward motifs. (B) Reverse complement of motifs.
Mentions: The top two predictions (q-value <0.01) were compared to known plant motifs in the PLACE database (Higo et al., 1998) using the STAMP web server (Mahony and Benos, 2007). The first motif (Fig. 3, m1) (q-value=4.4 × 10−9, information content=7.4) and the second motif (Fig. 3, m2) (q-value=1.1 × 10−3, information content=7.6) are similar to two experimentally characterized cis-regulatory elements found in the napA promoter in B. napus, the RY repeat (CATGCA) (E=6.32 × 10−8) and the G-box (CACGTG) (E=2.92 × 10−5) (Ezcurra et al., 1999). The function of these regulatory elements was shown by substitution mutation analysis using promoter–reporter gene fusions, leading to a strong reduction of the napA promoter activity in seeds (Ezcurra et al., 1999). The second motif is also highly similar to a sequence (ACGTGTC) (E=4.70 × 10−11) overrepresented in the promoters of A. thaliana genes downregulated during seed germination (Ogawa et al., 2003).Fig. 3.

Bottom Line: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters.The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.

ABSTRACT

Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.

Results: We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown to perform equally or better than other motif discovery tools. The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.

Show MeSH