Useful Web Services

• Michael Zuker's mfold server computes (sub)optimal structures and hybridization for DNA and RNA sequences with many options.
  http://mfold.rna.albany.edu/?q=mfold
• BiBiServ, several small services e.g. pseudo-knot prediction pknotsRG, bi-stable structures paRNAss, alignment RNAforester, visualization RNAmovies, suboptimal structures RNAshapes
  http://bibiserv.techfak.uni-bielefeld.de/
• The ViennaRNA Server offers web access to many tools of the ViennaRNA Package, e.g. RNAfold, RNAalifold, RNAinverse and soon RNAz
  http://rna.tbi.univie.ac.at/
• several specialized servers such as
  pfold consensus structure prediction
  http://www.daimi.au.dk/~compbio/rnafold/
  s-fold stochastic suboptimals and siRNA design
  http://sfold.wadsworth.org/ StrAl progressiv ncRNA alignment tool http://www.biophys.uni-duesseldorf.de/stral/

Web servers are also a good starting point for novice users since they provide a more intuitive interface. Moreover, the ViennaRNA Server will return the equivalent command line invocation for each request, making the transition from web services to locally installed software easier.

On the other hand, web servers are not ideal for analyzing many or very long sequences and usually they offer only few often-used tasks. Much the same is true for point-and-click graphical interfaces. Command line tools, on the other hand, are ideally suited for automating repetitive tasks. They can even be combined in pipes to process the results of one program with another or they can be used in parallel, running tens or hundreds of tasks simultaneously on a cluster of PCs.

You can try some of these web services in parallel to the exercises below.