My journal, Computers in Biology and Medicine. No fees, no page limits unless I impose them. Indexed in PubMed and Medline. Print and online editions. Mid level impact factor we're going to bring it up.
Bodhisattwa Banerjee mentioned this above, but I would just add for emphasis that the Journal of Computational Biology (JCB) is very well-respected among computational biologists and mathematical biologists and it does not charge for publication. There is a voluntary page charge, but publication does not depend on this. Like many other journals, they also have an optional open-source charge to make your article available to non-subscribers and the amount is pretty steep, $3200 I think. The point is that JCB has a publication option for everyone.
My journal, Computers in Biology and Medicine. No fees, no page limits unless I impose them. Indexed in PubMed and Medline. Print and online editions. Mid level impact factor we're going to bring it up.
You also need to consider the flip-side of the question. The cost of your paper to the readers.
Traditional journals need to make money (sometimes a lot), so if they're not charging for publication then they will charge for access.
Do you want people to read your paper? If so consider how easy it will be for them to do so. peerJ is an Open Access journal which means that all articles are free to read to all. Others will charge $20-40 for every reader unless their University or workplace has paid for them to get access.
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.
How much time does it take the reviewing process in your journals? I want to publish my plant related peptide based web server study. Can I submit my manuscript in this journal?