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Draw Map

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Tool description

Draw Map is a tool for visualization of protein sequence coverage after enzymatic or chemical digestion. It also allows you to compare the digestions with different proteases, under different conditions or for different times. It is also suitable for visualization of the results of limited proteolysis as it shows the structural elements and domains above the sequence and thus allow easy correlation of the cleavage sites with regions of higher accessibility.

It requires two simple text files as an input. Sequence file contains sequence of a protein and the Digest file contains the limits of peptides arising from the digestion. Optionally, you can use the Structure file which allows you to visualize structural elements (alpha-helix, beta-sheet) and domains above the peptide sequence in the resulting image.

Input fields

Sequence file

This file contains protein sequence in one letter code. Line breaks as well as lines beginning with > are ignored hence you can use your FASTA formatted sequence files. No check for validity of the characters is done so it is possible to use your own symbols, not only the 20 standard amino acid symbols. You can download an example sequence file.

Digest file

This file bears the information about the peptides. It can contain three or four columns. In the four column format the first column is used to differentiate between the conditions. Use abbreviations or continuous strings as any space will be considered as a separator. (e.g. PepsinDig, P, Pepsin are all fine but Pepsin Dig will be split into two columns). Second column can be used for your comments but is not considered by the script. The third and fourth columns represent starting and ending amino acid position of the peptide. In the three column format the second column is omitted so the first one is left for description of conditions, second for start and third for end of the peptide. Lines not containing integers either in second and third, or in third and fourth column are ignored. This gives you the opportunity to have column headers in the first line or some separator lines down in the file. Columns are separated by white-space characters (the best are space or tab). Example Digest files can be downloaded here – three columns, four columns.

Structure file

This text file is optional. You can use it if you wish to draw the structural elements (alpha-helix or beta-sheet) and domains above the sequence. It has five columns:

  • The first column contains either Str or Dom keyword. It tells whether the line encodes information about secondary structure or domain.
  • The second column contains the description of the structural element or domain (e.g. HelixA, Sheet1 or LipidBinding, etc.) There must be at least one character and the description should not contain spaces. Try to avoid long strings as they may not fit especially into short elements.
  • The third column encodes which type of structural element will be drawn – a stands for alpha-helix (cylinder) and b stands for beta-sheet (arrow).
    If there is the Dom keyword in the first column, this field is left empty.
  • The fourth and fifth column contain the first and the last residue number of described region respectively.

If the formatting of the line is not correct, warning message is written above the resulting image. You can download an example structure file.

Font

You can choose any TrueType font available on the server in this combo box. You can achieve the best results using condensed and narrow fonts.

Font size

Enter the desired font size in pt in this field. The lower limit is 6pt.

Number of AA's per line

This is the number of amino acids on one line. For example if you have 120 AA long protein and set 50 in this field, the result contains two lines with 50 amino acids each and the last line with 20 amino acids.

If you enter number lesser than 10 or a non-number entry, the default value of 50 will be used.

Thickness of bands

The thickness of the peptide representing bands in pixels. This number is the thickness of the color stripe itself, not including the black border.

If you enter number lesser than 1 or a non-number entry, the default value of 5 will be used.

Thickness of band borders

The thickness of the peptide representing band borders in pixels. This number is the thickness of the black border, so the real thickness of the band is twice this value plus value of Thickness of bands input field.

If you enter number lesser than 1 or a non-number entry, the default value of 2 will be used.

Width of one AA position

Here you can choose from three options - narrow, wide and normal. Narrow means that there will be only little space on both sides of AA letter, however the sequence will look compact. Another aspect of having narrow chosen in this field is that there will not be enough space for numbering of residues, thus this option is suitable only for shorter sequences or in combination with higher value of Numbering step input field.

On the other hand, choosing wide here gives you much more space for numbering or for example for latter hand-written notes to your printed picture.

Drawing priority

This option influences the way the tool assembles the bars representing overlapping peptides (often occurring in digests with non-specific proteases). In N-term nearest first it will take the set of overlapping peptides and align them from top to bottom with the peptide having N-terminal end closest to the N-terminus of the protein being on the top. The one closer to the C-terminus will be placed down. E.g. peptides 1-9, 5-15, 6-10 and 8-32 will be aligned in the order as they are shown here. In longest first the order of those peptides will be (from top to bottom) 8-32, 5-15, 1-9, 6-10. This option allows you to make your map more or less compact. Just test both and decide which result you like more.

Color scheme

Choosing grayscale here should result in better readable image printed using B/W printing devices.

Added N-term AA's / Start real numbering with / Added C-term AA's

These options are especially useful in case of recombinant proteins bearing tags or for constructs representing just a part of the native protein. It allows you to keep the native sequence numbering. If you have native protein or do not follow native sequence numbering leave the default values here (0, 1, 0 respectively). In other cases specify the number of amino acids added to the N- (Added N-term AA's) and C-terminus (Added C-term AA's) of the protein and define (Start real numbering with) from which amino acid in the native protein your construct starts. E.g. consider protein having 648 residues, your construct corresponds just to one domain (310-435) but has HisTag at the N-terminus (+12 residues) and three additional amino acids at the C-terminus. Then you will set Added N-term AA's to 12, Start real numbering with to 310 and Added C-term AA's to 3. In the resulting figure you will see the residues from HisTag numbered as from -12 to -1, C-terminal addition as +1 to 3+ and the numbering will start from 310 and end with 435.

Numbering step

Defines numbering of residues. By default the numbering occurs above each residue (numbering step 1) but it is often useful (for clarity of the resulting image) to use bigger numbering step, e.g. 10, 20 or 50.

Tips and examples

After the resulting image is created, it is displayed in your browser. If it is too large for your display, it is shortened. The easiest way to get the image is by right-clicking it and choosing Save image as... (or similar) from the context menu.

Another way to get the result is to click on "input file and result in tar bz2 file" link above the image and download the tar bz2 archive (could be unpacked using GNU Tar or 7-Zip) containing your input files together with the resulting image.

Dimensions in pixels (and roughly in milimeters at 300dpi) is displayed above the image. 300dpi is the resolution suitable for standard printing. If you need the image to be more narrow/wide, the Font, Font size, Number of AA's per line and Width of one AA position options should be adjusted.

You can see the example result.