As a bioinformatician, what would you consider the most prestigious venue for publishing your work? Would you prefer a first author paper in Bioinformatics instead of having name somewhere in a Science paper? Is PNAS more respectable than Bioinformatics? Would you allow your best work to be published in a conference proceedings instead of a journal?
As Michael Dondrup states, this is highly subjective. I think it depends largely on which side of 'bioinformatics' you come from.
As a biologist first, I (unfortunately) have followed the Science/Nature > PNAS > Current Biology/Cell > etc, etc. hierarchy. This has changed in recent years with new journals and more emphasis on open access publishing. In my opinion, citations are becoming a greater proxy for measuring prestige.
I'll never forget years ago when my old school mentor (with no computer experience) wanted to add more "bioinformatics" for managing the new burst of sequencing data we were getting from our department's new Sanger sequencer. We sat down as a research group with a new computer science professor who was looking for collaborations. My boss looked at his CV and asked him where his publications were. The new prof said "Here they are" and pointed to the spot on his CV. My boss says "These are all conference proceedings, they don't count as publications." This little story represents the divide that I think has existed in the "bio" and "informatics" side of the field in the past and maybe still exists.
I think the kind of publications you want will depend on what your career goals are. If these career goals are academic, you will want to (eventually) have your name in various places as an author. I view this from the biology side of publishing where you want to have papers with you as the first author (so you can prove you can do the majority of the work and make a research project come together), one of the middle names (to prove you can collaborate and work with others) and, eventually, last or managing author (so you can prove you can financially support and manage personel for the completion of a project).
The answer to you question depends on the career that you wish to choose and evaluation methods that come with it. There is no universally valid answer.
What if my career goal is to work for my dad's car towing company or IRS and like to publish an interesting result in a respectable journal just for the sake of publishing it? :) Should I post it at arxiv.org and let it be there? Does everyone publish with some reward from government in mind these days?
In each case people try to publish in journals that other people, similar to them consider as valuable. We tend to blame people at an individual level but they just respond to the incentives and requirements that they perceive.
My personal insight here that publishing in Nature is so difficult, stressful and tortuous that by the time I got there it turned me into the quintessential jerk reviewer towards others - in hindsight these were the worst times of my life - I would personally always strongly recommend against publishing on these avenues
But again these are personal opinions and I would not want to make blanket statements on how this might work out for everyone. A word of a caution though, I also met and worked with a lot of scientists that do more regularly publish in Nature, Science and they don't seem to be happier than those that don't.
I understand the question is subjective, but with audience of biostars and their voting power, I thought I could get some idea about which way the wind is blowing these days :)
Most of you may not like what I may comment- It is very tough to get a good publication just on computational basis. However the exception is Nature papers dealing with TCGA and every other GWAS studies in Natuer Genetics. These two kind of papers are just data generation, If you look at most of TCGA paper there is a disconnect between paper aim and biology just hand waiving. still Nature and other high impact journals take it. Similarly, GWAS you sit in your office collect samples cores will run those samples a poor bioinformatician will analyze and paper is out What next everyone--- know ; pick another association another Nature Genetics. No follow up on previous work. NIH has invested so much money on TCGA and GWAS. The point which I am trying to make is to get into a good journal you may have to be associated one of such grps it is piece of cake. However i leave it to you to judge about these publications and sooner or later they will be loosing following. If You realy want to contribute in science you may like to balance out between biology as well as computational approaches so that you can give to the community some good leads, even if you publish in an average journal. Nonetheless these are my thoughts you may like to choose science and not publication.
Best
If you want to get a good publication "just on computational basis", you're doing it wrong. An algorithm can be interesting or useful, but bioinformatics is about making biological discoveries. If you haven't applied your tool and come up with some new and fascinating insights into biology, then no, you can't expect to publish in a selective journal.
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This might become rather subjective, should it be forum instead?