Genome

“open” button – opens files with extensions: .gb, .gbk. 
“save” button – saves files with extensions: .gb, .gbk. 
“close” button – closes file, clean the graphical and sequence views. 
“print” buttons – print the content of graphical or sequence view. 

  • Graphical view
  • Sequence view
  • DNA features and annotation
  • DNA features databases and find features
  • Find motifs in DNA sequence
  • Find ORFs in DNA sequence
  • Transcribe, reverse complement and translate DNA sequence
  • GC content, CpG islands and stem loops
  • “text colour” and “background colour” buttons
  • Copy/paste the selected genome sequence with features
  • Open a protein from CDS in the Protein Tab or Alignment Tab
  • Open the selected genome sequence in the DNA or Alignment Tab

Graphical view
If the genome size is more than 1000 000 bp (1 Mbp), the genome graphical view is displayed as a scale without features. To see the features reduce the genome scale below the 1000 000 bp by clicking and dragging in the corresponding region of genome.
To zoom in or out, set the zooming size (top right of window) and press the “+” or “-” buttons.
To shift the view frame to the left or right side use the “<” and “>” buttons.
To return to whole genome view use the “return” button .
To search for a word present in the features descriptions use search field and the “<” and “>” buttons. The graphical view and the sequence view will automatically be changed according to the feature position where this word is found.

Sequence view
The genome sequence with features will be displayed when the genomic scale is less the 50 000 bp (50 kb).

DNA features and annotation
(Note. The graphical user interface is the same as for the DNA Tab)
Click on the featured region of the genome sequence and its features will be displayed in the “features” text field. To see the complete feature description, place the mouse pointer over the corresponding graphic element in the genome graphical view. Click on this element to highlight the corresponding sequence in the sequence view.
Use the “Features” button to display, edit and add DNA features. To select the features and colors to display in the genome sequence and Map, use the corresponding check-boxes and color wells, then press the “selected” button. To remove or to edit a feature, delete or change the corresponding text in the features window and press “save” button. Alternatively to delete a feature, select a text inside the feature and press the “delete” button. If the features were incorrectly edited, to restore all initial features press the restore features button . 
For the selected part of the genome, a new feature can be added from the features list or as a custom feature. Feature location can be typed or will be set automatically for the selected part of genome sequence. To mark the DNA strand as complementary use the checkbox “complementary strand”. Use the “add feature” button to add the feature.
Press the “features table” button to open the website with a complete list of genbank features. 
The edited features are not saved until the “save” button is pressed. 
Use the “Annotation” button to display and edit the anannotation. To save the annotation use the “save” button.

DNA features databases and find features
(Note. The graphical user interface is the same as for the DNA Tab)
Use the “Features Databases/Find” button to set the features databases and to find features in the DNA sequence from the main window.  
There are two custom databases: “Vectors” and “Genomes”. Features can be added to the databases from a genbank file when the corresponding checkboxes are On. The features of the same origin selected in the tables can be deleted by pressing the “delete” button. 
To find features, set the checkboxes and press the button “Genome”. The find function searches for exact matches of databases features and sequences. The databases can be exported and imported as text (.txt) files.  

Find motifs in a DNA sequence
(Note. The graphical user interface is the same as for the DNA Tab)
Use the “Find” button to search for repeats, palindromes, stem loops, “start…end” and arbitrary sequences. Searches will be applied to the selected part of DNA sequence.
To start a search press the “find” button and to cancel an active search use “cancel” button.
To clear the windows use the “clear” button. To save the found motifs as a text file, use the “save” button.
When the motif is selected it will be marked in the main DNA window. The selected motif in the DNA window will be unmarked when the selection in the “Palindromes”, “Repeats” or “Found Stem Loops / Start-End sequences” windows is cancelled. Use the color well to change the color of the marked motif in the main DNA window.
      Palindromes and repeats
Use the “length (bp): minimum” and “maximum” to set the minimal and maximal sizes of the palindromes and repeats to be located. When the checkbox “inverted” is set to “on”, the program will search for both direct and inverted repeats. If the checkbox “inverted” is “off”, then the program will search only for direct repeats.
      Any sequence
To find, mark and unmark any DNA sequence in the main DNA window, use the “find”, “mark” and “unmark” buttons. To clear the search DNA window, use the “clear” button. The positions of the found DNA sequence will be displayed in the “Found positions” window. 
      Start-End sequences
To locate a sequence using only starting and ending sequences, use the “start-end sequence” button and provide a “start” sequence and an “end” sequence in the corresponding windows. Also provide the maximal distance between the “start” and end” sequences.
      Stem Loops
To find stem loops in the selected DNA sequence choose the “stem loops” segmented button, set the parameters of stem loop and press the “find” button. 

Find ORFs in DNA sequence
(Note. The graphical user interface is the same as for the DNA Tab)
The “ORFs” button opens a popup window with options for searching ORFs in the DNA sequence shown in the main window. The “ORFs” search is applied to the selected part of DNA sequence. (The same functions are used for DNA1 and DNA2). 
Type a minimal ORF length in the textfield “ORF minimal length(bp)” to limit the ORFs length. 
Set the “minimal pI” and “maximal pI” to search for ORFs encoding the proteins with pI values between these limits. 
To choose the start codons for forward and reverse ORFs, use the “Forward:” and “Reverse:” popup menus. 
Use the “find” button to start the ORFs search. If in the “Forward ORFs” or “Reverse ORFs” windows the ORF sequence is selected the corresponding translated protein sequence and its features will be displayed in the “Protein” window. 
To translate all ORFs, use the “translate all ORFs” button. 
To clear the windows, use the “clear” buttons. 
To save the found ORFs as a text file, or the graphic view of ORFs as a pdf file, use the “save” button. To print the graphic, use the “print” button.

Transcribe, reverse complement and translate DNA sequence
(Note. The graphical user interface is the same as for the DNA Tab)
Use the “Tran/RevCom/Tran” button to convert a DNA sequence in the main window into an RNA sequence, to perform DNA reverse-complement conversion and to translate the DNA. 
The “Tran/RevCom/Tran” functions will be applied to the selected part of DNA sequence. When the reverse-complement sequence is selected in the popup window the corresponding proteins will be displayed. When a protein sequence is selected, the protein properties will be displayed. To change the translation frame, use the appropriate selection of the DNA sequence. 

GC content, CpG islands and stem loops
Press the “GC/CpG/SL” button to open a popup window with a GC content, CpG islands and Stem Loops plots for the selected DNA sequence. To view the plot of stem loops, set the “Stem Loops content” checkbox on.
Press the “SL settings” button to set the stem loop parameters. To change the window size of the plots use the corresponding slider. To save the plots as a .pdf file, use the “save” button, or to print – use the “print” button.

“text colour” and “background colour” wells
Use these color wells placed in the bottom left corner to color the text and the text background.

Copy/paste the selected genome sequence with features
The selected genome sequence can be copied together with features. For this, use the “copy” button. To paste this sequence with features, use the standard paste function. The alert window will ask if you would like to paste only the sequence or the sequence with features.
To empty the buffer containing the selected sequence and its features use the “empty” button.

Open the protein from CDS in the Protein Tab or Alignment Tab
To open the protein sequence in the “Protein” or “Alignment” tab, click on the corresponding CDS and press the buttons “Protein” or “Alignment”.

Open the selected genome sequence in the DNA or Alignment Tab
To open the selected genome sequence in the “DNA1”, “DNA2” or “Alignment” tab, select the corresponding sequence and press the “DNA1”, “DNA2” or “Alignment” buttons. 

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