Ori-Finder2.0

Ori-Finder 2 Tutorial for identification of oriCs in archaeal genomes


[Down] 1. Upload a complete annotated genome sequence in GenBank format.
[Down] 2. Upload a complete annotated genome sequence in Fasta format and protein table file in PTT format.
[Down] 3. Select a sequenced and annotated archaeal genome from NCBI genome database.
[Down] 4. Upload a complete unannotated genome sequence in Fasta format.
[Down] 5. Select motifs by taxonomy.
[Down] 6. Output Example.
1. Upload a complete annotated genome sequence in GenBank format. [Down]
  • Users could paste or upload a complete annotated genome in GenBank format. GenBank Flat File Format contains a wealth of information including nucleic acid sequences and associated annotations. For more details please visit http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html.
  • Please note that button of GenBank should be selected to inform the program the file format. [Example: GenBank]

2. Upload a complete annotated genome sequence in Fasta format and protein table file in PTT format. [Down]
  • Users could paste or upload a complete genome sequence in Fasta format, and upload its annotation file -- Protein Table Files (PTT format). FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences. The PTT file format is a table of protein features. It is used mainly by NCBI and all the PTT files of published genomes could be found in ftp://ftp.ncbi.nih.gov/genomes/. [Example: Fasta \ PTT]
  • Please note that PTT file must to be uploaded if the button of Fasta is selected.

3. Select a sequenced and annotated archaeal genome from NCBI genome database. [Down]
  • Select a NCBI-recorded genome sequence Pyrococcus abyssi GE5.
4. Upload a complete unannotated genome sequence in Fasta format. [Down]
  • Users could paste or upload a complete genome sequence in Fasta format. FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences.
  • Please note that you could select a gene-prediction tool to identify the protein-coding region. [Example: Fasta]

5. Select motifs by taxonomy. [Down]
  • Several motifs are provided to users by organism taxonomy, including Methanobacteriaceae, Methanomicrobia, Methanococcaceae, Sulfolobaceae and Thermococcaceae. Users could select one of them according to their needs.
6. Output. [Down] [Example]
  • As shown below, the location of oriC region with ORB sequence is the final result. Users could click it to browse detail information about the oriC.
  • The left figure shows the Z-curves (AT, GC, RY and MK disparity curves) for the original sequence. The right figure shows the Z-curves (AT, GC, RY and MK disparity curves) for the rotated sequence beginning and ending in the maximum of the GC disparity curve. Short vertical red line indicates the replication proteins location. The black arrows pointing below are the oriCs with ORB sequences, whereas the arrow pointing up is the oriCs without ORB sequences. Users could click to enlarge the image.

  • The detail information table about oriC. The ORB sequences are identified by FIMO tool. And the repeats are calculated by REPuter program.