Page1 : The HTML table
The HTML table provides the basic information of the genome and the simple predicted results.
Click the link marked in the red box, the website will jump to Page2 which presents the detailed information of the replication origin.
Click the pictures to see details.
Page1 : Figure 2
The Z-curve graph rotated at the maximum of the GC disparity curve.
Page2 : The HTML table
The HTML table provides some simple information of the oriC.
Page2 : Oric map
The oric map contains two parts.
The line graph with gradient colors shows stress-induced DNA duplex destabilization (SIDD) predictions calculated by SIST for the oriC sequence.
The transition probabilities displaying by five lines are calculated by different negative superhelicity values.
The region with high transition probabilities is susceptible to melting.
Therefore, the peaks may correspond to the AT-rich DNA unwinding elements (DUEs).
The second part is the schematic diagram of oriC sequence showing the distribution of the motifs.
Page2 : Oric sequence
The different motifs in oriC sequence are marked by different colors or symbols.
The red arrow indicates DnaA box, and its direction indicates the direction of the DnaA box.
The orange and blue underline indicate spacer and DnaA-trio in the basal unwinding system, respectively.
The Dam methylation sites (GATC) and the CtrA binding motif are displayed in red and green, respectively.
The red wavy line indicates the possible AT-rich DUEs corresponding to the maximum of transition probabilities.
The indicator genes upstream and downstream of the replication origins are marked on both sides of the oriC sequence.
Page2 : Repeat sequences discovery in oriCs by MEME
In order to reveal possible new motifs, the repeat sequences in predicted oriCs are discovered by MEME.
Page2 : The distribution of genes on leading or lagging strand
Page2 : The distribution of base composition on leading or lagging strand
The Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Purine (A+G) and Pyrimidine (C+T) content as well as sequence length of the leading strand and lagging strand are counted here.
Page2 : Homologous oriC sequences search with BLAST
The homologous sequences to predicted oriCs are searched by BLAST against the DoriC database, and the BLAST results linking to the corresponding entry in the DoriC database are also provided.