- The MPI Bioinformatics Toolkit for protein sequence analysis

As this special issue shows, the number of public bioinformatictools and web servers is growing quickly. However, the wealthof powerful tools and servers is, in our opinion, only utilizedby a fraction of biologists who would be able to profit fromthem. Especially for non-experts it can be very time-consumingto find out which services exist, what they can or cannot do,how to use them and how to feed results from one service tothe next in the right format. This has spawned the developmentof two classes of servers. The first class, exemplified by PredictProtein(1), accepts a single sequence as input, runs a whole set ofstandard protein analysis tools and returns the bare, concatenatedresults in a single Email or Web page, requiring users to befamiliar with the tools and their output format. The secondclass offers a collection of web interfaces to local versionsof public bioinformatic tools. For instance, PAT (protein analysistoolkit) (2) facilitates the combination of different analysismethods by automating repetitive data processing tasks. However,its user interface and the lack of an integrated help systemmake PAT, suited primarily for users with biocomputing experience.Two further servers designed as toolboxes for sequence analysisare the Biology Workbench (3), which has not been updated forquite some time, and AnaBench (4), which is more geared towardanalysis of DNA data.

The primary aim in developing the MPI Bioinformatics Toolkitwas to offer a web service that is as easy to use as possibleand that integrates a selected set of most useful methods forthe analysis of protein sequences. From our own experience asusers of the toolkit, its main advantages are as follows:

  • In-housetools: Several programs developed in our group areavailableonly through our toolkit, e.g. HHpred (5), HHrep (6),HHsenser(7), REPPER (8), CLANS (9) and Blammer (10) (see Table 1).
  • Enhancedfunctionality of public tools: Many tools offer additionalfunctionalitycompared with the original public server (seetool descriptionsbelow).
  • User databases: Users may upload customized databaseswhichare then accessible throughout the whole toolkit (uploadonce,use many times).
  • Interconnectivity: Most of the toolsin the Toolkit are interconnected,allowing job results of onetool to be forwarded as input toothers.
  • Streamlined, uniformuser interface: Input forms are kept assimple and self-explanatoryas possible with a uniform designand logic for all tools.
  • Straightforwardnavigation: Tools are grouped into color-codedsections thatare easily accessible via tabs.
  • Job management: A dedicatedjobs sidebar provides informationand quick access to all jobresults of the current session.
  • Personal work space: Usersmay register and log in to gain accessto a personal work spacefeaturing long-term storage of jobs.

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