JaMBW Chapter 3.1.5

ORF Seeker

Aim

Given a sequence of nucleic acids and a translation table, this program generates all the corresponding aminoacid sequences, for each potential open reading frame.

Mode of operation

The program uses three windows: the top one should be filled from the user, with a sequence of interest, while the other windows contain the results of this frame analyis. The following steps must be performed:

Choice of translation table
The official translation tables as compiled by A.Elzanowski and J.Ostell (1996) are made available through this applet by a simple pull-down menu. In order to choose a translation table the user has simply to select it from the available list through the pull-down menu. User-provided translation tables are supported by the parameter mechanism of the applet, without need of modifying the program, details are provided in the html source of the page.
Sequence input
- Symbols used
  Either paste or type in the top area the sequence of interest. Any character or symbol that does not belong to the [atcgATCG] set is ignored.
- removal of header information
  Only the sequence must be placed in the top window: heading comments must be removed
- long sequences and small window
  In order to allow users with small screens to still be able of using this program, the size of each window had been made rather small. Therefore, use the scroll-bars in order to move around in the input and output windows. The suggested strategy is to double click in the specified area and then do copy/paste from/to the text-editor of choice or across different applications.
Compute
Once the sequence is placed in the top window, by pressing the "COMPUTE" button all the Open Reading Frames are computed and visualized.