WAViS: help page


Server functions

WAViS generates pictures of your alignment files.
Two main methods are available:
  1. Bitmap alignment scheme
  2. Vector similarity graphics
There are additional options and small utilities for handling biological sequences.

File formats

The server is capable of using several input data-file formats, namely:
Several output formats can be generated:
You can find extensive description of most common alignment formats in link 1, link 2

Generating picture

To get familiar with this server, see the following examples.
Download this alignment, in the multi-FASTA format.

mfa-preview

Store it in your computer.

Select "Alignment scheme drawing (bitmap graphics)" link at WAViS server in your browser.

Click "Browse" to select your stored (example) file.

Set properties of the picture:

picture width: 500
sequence width: 15
border width: 15
base line border: 25
show labels: checked
sort by length: unchecked
generate EPS: unchecked
compress EPS: unchecked
).

Click "Preview" button, you can see a simple presentation of your alignment (ignoring your settings).

Click "Upload" button.

Check your parameters and set "Highlight region" options. To get the same picture as in this example, choose

All -> 100 -> 145 -> NavyBlue
1202290 -> 0 -> 16 -> SpringGreen4.

Click "Draw" button. You should get the following output:

alignment picture
Download alignment unless you did in previous example.

Select " Similarity drawing (vector graphics)".

"Browse" the file with mfa-formated alignment.

Set options as follows (default parameters):

Show consensus sequence: checked
Numbering based on consensus position: checked
Num. of characters in row: 50
Num. of characters in nest: 10
Compress output with: unchecked

Click "Convert" button.

In the case your browser is not capable of viewing SVG graphics we provide bitmap view of the result (newer browsers such as Mozilla may optionally show this type of pictures). SVG graphics can be imported  and handled in vector-based programs such as Corel Draw, Adobe Illustrator, Sodipodi.

svg-preview

Credits

Server scripts, command-line frontend and library are written in Powered by PERL