JOY5 is a new version of JOY, written from scratch in ANSI C with significantly enhanced functionalities. Most features supported in the previous versions have been implemented now. The IRIX, LINUX and SPARC binaries are available (go to download). If you would like to try it out on other platforms, please contact me.
The following HOWTOs demonstrate various new features:
Your input .ali file can include the sequence of proteins both with and without 3D structural information. Each entry begins with the line
where code is a unique ID for the protein. You can use any number of alpha-numeral characters, hyphens ('-') and underscores ('_'), but at the moment PostScript output uses the fixed-width title field so you may want to avoid very long IDs. More flexible PostScript output will be available soon. The next line is either
If the word structure appears here, JOY looks for datafiles for structural information and annotates each amino acid residue according to its structural environment. If no structural information is available, simply put the word sequence. The actual amino acid sequence begins from the third line. Thus, this .ali file produces the following output files (HTML, PS).
By default, the residues of sequence only entries are coloured using the Taylor colours (Protein Eng. 10:743-746 (1997)). This feature helps examine amino acid conservation along with the structural environments of one or more homologues. Other colours can be chosen by typing:
--seqcolour=0 (no colour) --seqcolour=1 (clutalx colours) --seqcolour=2 (Zappo colours)
For example, typing
joy --pscolour fn3.ali
will produce the above output files, while
joy --seqcolour=0 fn3.ali
will produce a black and white PS file.
Sequence only entries are shown in a smaller font. You can increase or decrease the fontsize for sequence by typing:
joy --seqfontsize=10 --pscolour fn3.ali
You can also display sequences in lower-case letters:
Compare this with this
It is now possible to prepare an alignment for parts of the proteins and annotate it as if the residues are in their original structural environments. The .seg file is no longer required. This is useful, for example, when you generate a structure-based alignment for the protomers of olibomeric proteins but want to display the structural information (accessibility, H-bonds, etc) in their original biological units.
Here is HOW
structureX:1hslad1: 1 :A: 91 :A:undefined:undefined: 1.89:19.90
The easiest way to produce this is by typing
Now you have the file dom1full.ali
You can change font size and alignment width.
Example 1 (HOW)
Example 2 (HOW)
For HTML output, background colour can be changed as well:
Example 3 (HOW)
For PS output, you can also use different fonts: try joy --psfont=font
where font can be times, helvetica or courier.
To undisplay 'Key to JOY', type
To undisplay alignment position, type
Instead, you can add the line '>N1;!code' in your .ali file. This will display the PDB residue numbers of the specified protein at the top of alignment, as well as insertion codes (A, B,...) where gaps occur with respect to this entry.
To undisplay consensus secondary structure line at the bottom of alignment, type
JOY requires datafiles (.psa, .sst and .hbd files) for all the
structures in the alignment, but you don't have to have these
files in the current directory. Type
joy --dir=directoryand JOY will look for the datafiles in the specified directory rather than the current directory.
By default the sequence names are truncated at the tenth charcter
in both HTML and PS output. You can change this number ty typing
joy --maxcodelen=20then the first 20 charcters are retained. To retain all the characters, specify zero or a negative number.
Some programs such as CorelDraw and Adobe Illustrator can read in PostScript files. JOY5 now produces a Rich Text Format file (.rtf) which can be read in to Microsoft Word and other software (example). The RTF output, however, is still experimental and not all the features are supported.
Miscellaneous new features
|Display domain information (HTML only)|
Shading secondary structures in black and white PostScript output
Any number of sequences, residues and any number of characters for protein codes
More efficient and robust HTML and PostScript code (the size of HTML and PS files have been significantly reduced)
Output different types of structural features
Simply type joy to display all available options
The following features, tried in earlier developments, are currently suppressed:
|Display residues that are covalently bonded to co-factors|
|Overline to represent sidechain-sidechain hydrogen bonds in HTML output|
The annotated alignments in HOMSTRAD are now produced by JOY5.
NOTE: Many of the new display features above are rendered with HTML4 and at the moment, only a few browsers can display them properly. For example, Netscape (even Communicator 4.6) does not seem to display overlines, but the other features can be shown properly with Navigator 4.08. Microsoft Internet Explorer 4 displays both overlines and background colours.
Kenji Mizuguchi ( email@example.com)
Last modified: 01/08/02