OrientationChecker is a simple, quick tool for checking, and
if necessary altering, the orientation of 16S rRNA gene sequences.
It can also identify the location of partial gene sequences
within
the 16S rRNA gene sequence.
Figure 1. OrientationChecker screenshot (as viewed on
Microsoft
Wondows XP).
For example, consider a FASTA formatted file of sequences
varying in orientation and position within the 16S rRNA gene.
1) Loading this file into the program and
clicking Check
Orientation
generates the following display:
Figure 2. Display detail illustrating the orientation
and
positions (relative to the complete 16S rRNA gene) of partial sequences
contained within input file. Sense
orientation is indicated by a icon, whilst antisense is
represented by a .
2) Clicking Convert All Antisense to Sense changes all
antisense sequences to their sense counterpart:
Figure 3. Display detail with the antisense sequences
2 and
5 now
converted to sense.
3) All partial sequences of roughly the same length and location
can be selected and then saved to a separate file:
Figure 4. In this example, all partial sequences
located at
the 5'
end of the 16S rRNA gene have been selected. These selected
sequences can now be saved to a separate file.
icon, whilst antisense is
represented by a 
.
