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IMC J04A Extract ORF Candidates from Current Genome Sequence

Extract ORF candidates from the unnotated current genome sequence.

Operation

The genome sequence from which ORF is extracted is displayed as the current sequence in the main feature map.

From the menu click Genome Analysis -> ORF -> ORF Extraction ....

The "Range Setting" dialog will be displayed.

Check "Only longest ORFs are extracted in case of overlap".

Click "Run".

A confirmation message "Start ORF Search?" is displayed.

Click "Yes".

The "ORF Site" dialog is displayed.

The ORF candidate extracted is classified into three types, Long, Middle and Short, depending on its base length.

You can change the range of Long, Middle, Short base length range here.

In the left pane, the number of extracted ORFs by this base length is displayed.

If you check the checkbox in the left pane, ORF candidates belonging to the base length classification checked in the right pane are displayed.

It is also possible to check only the long ORF candidates at first.

The button on the lower side of the right pane is a button for selecting a check box.

Click "Select All".

All ORF candidates in the right pane are checked.

Click "Insert New Feature".

A confirmation message "Insert New Feature?" is displayed.

Click "Yes".

The ORF candidate is registered in the current genome sequence.

A completion message is displayed.

Click "OK".

ORF candidates are registered in the main feature map and displayed.

If the "ORF Site" dialog is open, clicking on one of the ORF candidate lines highlights the corresponding ORF candidate feature on the feature map and automatically scrolls the feature map horizontally (possibly not scrolling).

If you want to save the information of the registered ORF candidate, save using the "CSV ..." or "Fast A ..." button.

At this time, only the items checked in the checkboxes of each column are saved as files.

From the menu click File -> Save ... to overwrite the current genome sequence.

At this time, FastA file is automatically converted to GenBank or EMBL file.

If you exit without saving, the ORF candidate feature registration will be discarded.

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