Fig 1.
Web interfaces of RNA secondary structure prediction results.
The web page shows the nucleotide sequence, genic annotation, DBN data, and secondary structure graph. In particular, the sequence segments with different annotation features (i.e., 5’ UTR, CDS, intron, 3’ UTR, etc.) are labeled with different colors. For demonstration purpose, we used the motif search function to search for the motif “[UC]CA[UC]” in this sequence, and found 1 match, which is highlighted in the nucleotide sequence, DBN data, and secondary structure graph correspondingly.
Fig 2.
Secondary structure graphs of selected mRNA isoforms and un-spliced mRNA in Arabidopsis.
(a) mRNA (Ensembl ID “AT4G27800.1”). (b) mRNA (Ensembl ID “AT4G27800.2”). (c) mRNA (Ensembl ID “AT4G27800.3”). D: un-spliced mRNA (Ensembl ID “AT4G27800.1”).
Fig 3.
Secondary structure graphs of selected ncRNAs and ssDNA in Arabidopsis.
(a) lncRNA (Ensembl ID “AT1G04425.1”). (b) miRNA (miRBase ID “MI0031741”). (c) miRNA (miRBase ID “MI0031741”) with customized annotation information (star miRNA position). (d) ssDNA (chromosome: 1; start: 200; end: 400; strand: +).
Fig 4.
Secondary structure graphs of a selected rRNA in Arabidopsis.
(a) rRNA (Ensembl ID “ATCG00920.1”) without experimental data as constraints. (b) rRNA (Ensembl ID “ATCG00920.1”) with experimental data as constraints.
Fig 5.
Genome browser views of a randomly selected region in Arabidopsis thaliana genome.
(a) BrowserGenome view of the selected region (chromosome: 1; start: 9929905; end: 10027295). (b) JBrowse view of the selected region (chromosome: 1; start: 9929903; end: 10027293).