“open” button – opens files with the extensions: .txt, .rtf, .fasta (.fas, .faa), .seq, .gp, .blprotein.
“save” button – saves files with the extensions: .txt, .rtf, .fasta (.fas, .faa), .seq, .gp, .blprotein. 
“close” button – closes file and clean all related windows. 
“print” buttons – print the content of the main window or the peptides table.

The blprotein file format is a custom text file format combining rtf and gp formats. For details, see the bldna/blprotein and blalignment file formats description.

The buttons “SS Prediction/PDB”, “Hydropathicity/pI Plots”, “Features”, “Annotation”, “Limited Proteolysis”, “SS database” open pop up windows. A mouse click outside of the popup window will close the window, and a click and drag action will generate a separate window.. 

  • Protein parameters
  • Prediction of protein secondary structures
  • Reverse translation
  • Hydropathicity/pI plots
  • Features and annotation
  • Limited proteolysis
  • “text colour” and “background colour” buttons
  • Mark and unmark amino acid residues
  • Mark and unmark protease sites
  • Mark and unmark peptides
  • Open a selected protein sequence in the Alignment Tab
  • Format protein sequence

Protein parameters
The protein parameters: pI value, MW, net charge will be automatically displayed for the whole protein or for its part after the corresponding sequence selection. The amino acid composition of protein is displayed automatically for the whole protein in the “Amino Acids” table.

Prediction of protein secondary structures
Press the “SS Prediction/PDB” button to perform the prediction or to see the protein secondary structures from a PDB file, and to display the coloured protein sequence in the popup window.
Before, press the “SS database” button to open the popup window to set the protein secondary structures databases.
The default database used for secondary structure prediction is that for mesophilic organisms (cytoplasm and membrane locations), but other databases can be available that may be more appropriate (e.g. for halophilic proteins). These databases should generated by user from the pdb files and may be useful for the analysis of particular types of proteins, e.g. when proteins belonging to the same protein family, or proteins in the same cellular location (membrane/cytoplasme) or environment (halophilic, mesophilic, thermophilic). To delete a custom database, set the corresponding checkbox on and press the “delete” button. 
The databases can be exported as text files. The created file of the custom databases can be imported. For this, use the “export”, “import” buttons. Add the custom databases for analysis by setting the corresponding checkboxes.

Reverse translation
Pressing the “RevTran” button opens a popup window with a reverse translated gene sequence optimised for highest codon usage frequency.

Hydropathicity/pI plots
Pressing the “Hydropathicity/pI Plots” button opens a popup window with hydropathicity and pI plots for the opened protein sequence.
Set the “Hydrophobicity”, “Hydrophilicity” and “pI value” checkboxes to see the corresponding plots. To view the protein secondary structures underneath these plots, set the “SS prediction” checkbox to “on”, or the “SS from PDB” checkbox to “on” when a PDB file is opened. 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.

Features and annotation
Click on the featured region of a protein and its features will be displayed in the “features” text field.
Use the “Features” button to display, edit and add protein features.
To select the features and colors to display in the protein sequence, 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 protein part a new feature can be added from the features list or as a custom feature.
Feature locations can be typed or will be set automatically for the selected part of the protein sequence. Use the “add feature” button to add the feature.
The edited features are not saved until the “save” button is pressed. 
In the “Annotation” window, an annotation from .gp, .blprotein, or .fasta files can be displayed, edited and added.
To save the annotation use the “save” button

Limited proteolysis
Press the “Limited Proteolysis” button to see the list of peptides resulting from limited proteolysis for a protease selected in the table “Present Enzymes Sites”.
The list contains the peptides sequences and their masses in parenthesis. 
To see the location of a peptide in the protein sequence and a peptide pI value, select the peptide sequence. To unmark the peptide sequence cancel the selection.

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

Mark and unmark amino acid residues
To mark amino acid residues in a protein sequence, select the corresponding row in the “Amino Acids” table.
To unmark all amino acid residues use the “all” button. To unmark particular amino acid residues, select the corresponding amino acid residue in the “Amino Acids” table and then press “selected” button.
To change the color of the marked amino acid residues, first unmark them, change color in the corresponding color well and then mark them.

Mark and unmark protease sites
To mark protease cut sites in a protein sequence, select the corresponding row in the table “Present ES”. The selected protease name will appear in the table “Selected ES”.
To unmark all protease sites use the “all” button. To unmark particular protease sites, select the corresponding protease in the table “Selected ES” and then press “selected” button.
To change the color of the marked protease sites use the corresponding color well.

Mark and unmark peptides
To mark the peptides, select the corresponding row in the peptides table.
To unmark the selected peptide use the button “unmark”.

Open a selected protein sequence in the Alignment Tab
To open the selected part of protein sequence in the “Alignment” tab select the corresponding sequence and press the “Alignment” button.

Format protein sequence
Use the “format” button to remove colors, line breaks and white spaces in a protein sequence.

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