This is not so easy to answer. In terms of impact factor and prestige, I agree with Bioinformatics and NAR, but the real nitty gritty of bioinformatics research is done online and using community based systems. For example, I have been citing this Love and Anders paper in some grants and papers, but it is only available here:
Also, you often find resources online for bioinformatics that are not really publications, but instructions or pipelines. Are you looking for a place to publish? That is a different question, I guess.
This link contains a sufficiently good list of journals with links to their homepage.
http://www.bioinformatics.org/wiki/Journals
Some may come under the name of computational biology, you should check those out too.
BMC Bioinformatics is a good journal, Genome Biology is a good one too,
Start from the above list, have a look at their impact factors, but most importantly take some time and read articles in these journals and decide if they are suitable for you (in case you want to publish for example).
The research on Bioinformatics is increasing tremendously. All reputed Journals either will charge heavily or may not accept without experimental proof (wet lab).
With the intention to publish the dry lab work with no processing fee, we started a Journal called International Journal of Computational Biology and Bioinformatics (IJCOB), Strings Publications.
http://www.ijcob.stringsjournal.com/
Being the editor-in-chief of IJCOB I request you to share your manuscript and publish in IJCOB.