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Results: 5

1.
Figure 4

Figure 4. From: Hundreds of putatively functional small open reading frames in Drosophila.

Distribution of the 4,561 smORFs conserved in D. pseudoobscura. Venn diagram representing the distribution of the smORFs with start and stop codons in D. pseudoobscura and passing each of the different validation filters, and their combinations. Each circle is proportional to the size of the population it represents. Dp, D. pseudoobscura; Ka/Ks, ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitution.

Emmanuel Ladoukakis, et al. Genome Biol. 2011;12(11):R118-R118.
2.
Figure 1

Figure 1. From: Hundreds of putatively functional small open reading frames in Drosophila.

Search pipeline for Drosophila smORFs. Diagram of the smORF search pipeline followed in this study. The percentages of smORFs passing each filter are indicated. For full details, see Results and Materials and methods. CDS, coding DNA sequence; Dm, Drosophila melanogaster; Dp, Drosophila pseudoobscura; Ka/Ks, ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitution.

Emmanuel Ladoukakis, et al. Genome Biol. 2011;12(11):R118-R118.
3.
Figure 5

Figure 5. From: Hundreds of putatively functional small open reading frames in Drosophila.

Relaxed pipeline for smORF search. Pipeline for search of smORFs with the lowered E-value < 0.05 threshold for the tBLASTn filter. Despite an initial higher percentage of smORFs passing this filter, subsequent results are similar to those obtained by the initial stricter pipeline shown in Figure 1. For details see text and Materials and methods. Dp, D. pseudoobscura; Ka/Ks, ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitution.

Emmanuel Ladoukakis, et al. Genome Biol. 2011;12(11):R118-R118.
4.
Figure 3

Figure 3. From: Hundreds of putatively functional small open reading frames in Drosophila.

Cumulative size distributions of smORFs with conserved start and stop codons. (a, b) Size distributions (represented as cumulative graphs) for the putative D. melanogaster smORFs with tBLASTn E-value < 1 × 10-3 (a) or < 0.05 (b), and conserved, in-frame start and stop codons in D. pseudoobscura (SS), and their respective controls composed of reverse stop-to-start control 'smORFs' passing the same filters. The candidate 'real' smORF distributions are very different from the controls representing random short DNA sequences. For a statistical analysis of the differences between these distributions, see Additional file 1.

Emmanuel Ladoukakis, et al. Genome Biol. 2011;12(11):R118-R118.
5.
Figure 2

Figure 2. From: Hundreds of putatively functional small open reading frames in Drosophila.

Size distributions of different pools of smORFs. The size distribution of different pools of smORFs is represented according to their length in codons. Medians are indicated. (a) 43,197 smORFs with tBLASTn hits with E-value < 1 × 10-3 representing putative smORFs with some kind of sequence conservation in D. pseudoobscura. Mean size = 44 codons, standard deviation = 12. (b) 4,561 putative smORFs with conservation of sequence and start and stop codons in D. pseudoobscura, representing our upper estimate for the number of smORFs in Drosophila. Mean size = 25 codons, standard deviation = 12. (c) 1,075 smORFs with syntenic conservation, and start and stop codons in D. pseudoobscura, and with a Ka/Ks (ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitution) score < 0.1. Mean size = 19 codons, standard deviation = 8. (d) 401 smORFs with conservation of sequence, and start and stop codons in D. pseudoobscura, with a Ka/Ks score < 0.1, and also present in transcribed regions, representing our conservative estimate. Mean size = 21 codons, standard deviation = 12. For a statistical analysis of the differences between these distributions, see Additional file 1.

Emmanuel Ladoukakis, et al. Genome Biol. 2011;12(11):R118-R118.

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