One fairly common task is to make some sequences available for BLAST search over the web. So far, this has meant installing the NCBI web front end to BLAST, but this is something like 15 years old, and it shows. Although we have some local enhancements that allows the user to click on sequence names to download them, etc, I really would like a more flexible replacement. Surely something more advanced exists? Something equally easy to download and set up?
Edit: To be more specific, I would like a user friendly (i.e. simple) interface to do sequence search (not necessarily BLAST) against our own sequence data. Features I'd like to see might be
(Feel free to suggest additions to the list in the comments below!)
You can have a look at SequenceServer too. Its easy to deploy, and has an intuitive UI. Currently in 'Beta 1' it supports:
On TODO is:
And SequenceServer is open source.
Oh, and I forgot to mention you can enter other (advanced) parameters too as you would from the command line. So you can blast with different evalue settings, or change num_alignments.
(FYI there's been quite a few updates since this...)
If by 'user' you mean some skilled bioinformaticians, I would create a WEB-Service (WSDL+SOAP/REST) to let them play with your data as they want without having to connect to your HTML interface. You can find this kind of service thought the biocatalogue.org . For example: http://www.biocatalogue.org/services/47
If you really need a new kind of web interface (why?), I would play with a nice javascript framework (GWT, ...) to create an interactive experience.
No, I guess not, it's there to provide an interface to BLAST, I replied to this before you updated your answer. Your feature list doesn't seem unreeasonable, but you're really talking about post-BLAST processing. I think the point about Mobyle is that you could, if you so desired, customise it for your requirements.
ViroBlast is a easy to set up web interface for BLAST. Compared to NCBI's web front end it is only slightly more flexible, but at least it looks more modern. It can be obtained for free for academic use.
http://bioinformatics.oxfordjournals.org/content/23/17/2334.abstract
This is fairly close, although not terribly feature laden. It seems to cover #7, and provides links to genbank - it's unclear if I can link to my own sequences, and there's no visualization. I'd prefer something with a standard license, but I guess it's not a show-stopper.
You might like to look at Pise. It allows you to create web interfaces to any command-line program including BLAST, quickly, using config files in XML format. It comes with scripts that automate the build, given the command-line arguments.
It's been around for a while so I don't know whether it works with the very latest BLAST. The interface is quite basic - not a whole lot more than you'd get from the NCBI web package, but may have more options for customization.
Another option - depending on how much work/time you want to invest - is to roll your own, which is very simple these days with modern web frameworks such as Rails (Ruby) or DJango (Python).
I'd also suggest that you consider whether provision of web interfaces is a good use of your time. It's quite a lot of work and maintenance (of the boring sysadmin variety), just to make life a little simpler for a few users who probably won't even appreciate it. Sometimes I think it would be better (as in more useful and educational) to set up BLAST on a server, provide SSH access and run a short course/tutorial on the basics: logging in, running a command-line BLAST and saving the results, then provide some basic parsing scripts.
I see we had the same thought ;) But PISE is superseded by Mobyle now https://projets.pasteur.fr/wiki/2/Download
Sometimes they might do it in a better and more standardized way and use ... an Excel sheet
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Hey Ketil, please check out Anurag's answer below (https://github.com/yannickwurm/sequenceserver). If fullfills 2,4,5,6,7. Advanced blast params should make 3 possible (but would require smart users). www.sequenceserver.com remains to be updated as of 2011.06.06)