Is this the case when the genes are transcribed in the opposite direction (reverse complimentary) on the non-coding strand and in the same direction but on the non-coding strand (complimentary)?
I base the orientation on the sequence on the form and position of ATG and TAA sequences (in Bacteria).
To my knowledge, genes are usually presented in 5'->3' direction, cause this is how RNA is transcribed. In fact, DNA strand during transcription is read 3'-5' (template, non-coding strand). A template strand for the gene going in one direction becomes non-template strand for the genes going in other direction. In the databases, you have to choose the direction, and some genes will go forwards, other backwards. The latter are rev comp I guess. Textbooks or smarter people could probably explain it better than me.
My guess is because only one strand of the DNA of a particular gene region could be sequenced with a specific primer and perhaps a primer for the complimentary (actually transcribed) strand was not a possibility.
The gene can only be transcribed from one strand as Lech already pointed out. But because the sequence was of the complimentary strand and you can't be completely sure of no discrepancies between the two it has to be marked as complimentary.
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