Sample result
  • The predicted results are usually presented through two pages(Page1 and Page2). After the prediction is completed, the website first jumps to Page1 which presents the basic information of the genome and the simple predicted results. Click the link of the replication origin on Page1, the website will jump to Page2 which presents the detailed information of the replication origin. There may be multiple possible replication origins in a genome. Each replication origin links to its own Page2.
  • Users can view the predicted result of the sample data by visiting
    the url http://tubic.tju.edu.cn/Ori-Finder2022/public/index.php/retrieve/sample_result The predicted results are explained in detail below.

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.

tutorial
Click the pictures to see details.

Page1 : Figure 1

  • The Z-curve graph with oriC related information. The red, green, blue and yellow line graphs indicate AT, GC, RY and MK disparity curve, respectively. The red, dark blue and light blue dotted lines indicate the locations of indicator genes, replication origins and replication terminus, respectively. The purple vertical lines indicate the DnaA box cluster. Users can zoom the figure by sliding the mouse wheel or select specific datasets of interest for observation by clicking on the legend below. Moreover, when users hover the cursor over the dotted lines marking the predicted oriCs, indicator genes or replication terminus, the exact location and other information will be auto-displayed.

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    Page1 : Figure 2
    The Z-curve graph rotated at the maximum of the GC disparity curve.

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    Page2 : The HTML table
    The HTML table provides some simple information of the oriC.

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    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.

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    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.

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    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.

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    Page2 : The distribution of genes on leading or lagging strand

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    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.

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    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.

    tutorial