I am often caught between sending papers to specific informatic journals or specific biological journals.
I think it's depend upon your work. If your work is more biological then you can publish it in biological journal. But most of the time biological journal ask for some biological experiments, but in computational genomics they are still publishing. If it's more or less computational biology work then you have to look Bioinformatics journal, if it's pure theoretical work then you have to look for informatics journal.
I agree, but I'd say it also depends on your target audience.
If you are publishing a bioinformatics tool that would be accessible to a wider audience and you want to encourage other researchers to use it, for example predictions of phosphorylation sites, then I'd aim for a more general biological journal. That way researchers that would want such a tool but not generally go looking for such things outside their general literature pool will see it.
However, if it's more technical/theoretical work involving improvements in methodology, for example, then a bioinformatic journal would be more appropriate.
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