1. 1 EMBL Outstation — The European Bioinformatics Institute EDITtoTrEMBL Automated High-Quality Sequence Annotation Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler

2. 2 EMBL Outstation — The European Bioinformatics Institute We Need Rules F Rephrasing of primary annotation to terms of the restricted vocabulary of SWISS-PROT F Constraints to ensure correctness Analyser: F Queries to database or execution of program F Application of rules

3. 3 EMBL Outstation — The European Bioinformatics Institute Rules on a Higher Level F Resolving inter-dependencies between Analysers F Integrity checks F Redundancy detection Dispatchers: F Communication between analysers F Application of rules

4. 4 EMBL Outstation — The European Bioinformatics Institute Framework: Analysers+Dispatchers F Bidirectional communication between Dispatchers:Determine Dataflow Analysers:Create Annotation

5. 5 EMBL Outstation — The European Bioinformatics Institute Multilevel architecture F Specialisatio n F Easier maintenance

6. 6 EMBL Outstation — The European Bioinformatics Institute Description of Analysers F Regular expressions to describe Õ Mandatory input é Quality-improving input Example: Prediction of transmembrane regions  /^SQ/ needs access to sequence  /^FT ([0-9]+) +([0-9])+ +SIGNAL/ influenced by proteins that have a signal  KW TRANSMEMBRANE FT TRANSMEM 0 0 F A string to describe Ö Expected Output

7. 7 EMBL Outstation — The European Bioinformatics Institute Workflow F Only a subset of analysers are active –if they have not yet performed on entry and all mandatory input is available –they have already performed and the entry was changed in regions of its mandatory or optional input F Rules determine sequence –analysers with all expressions matched first –analysers not expected to perform optimally later –analysers that might improve their annotation again –analysers that can be inhibited last

8. 8 EMBL Outstation — The European Bioinformatics Institute Termination at Fixpoint F Ambiguities should not influence final annotation F Termination: A point will be reached at which no further annotation can be added

9. 9 EMBL Outstation — The European Bioinformatics Institute Mutual Exclusion CC if not KWKW if not CC u Only one of these analysers annotates correctly u If two active analysers inhibit each other

10. 10 EMBL Outstation — The European Bioinformatics Institute Application F Current release built within EDITtoTrEMBL F next –Pfam –PRINTS F Analysers implemented –PROSITE –ENZYME –SignalP –TMHMM –MEMSAT

11. 11 EMBL Outstation — The European Bioinformatics Institute Implementation F Java using Remote Method Invocation –wrapping of legacy applications –distribution over the network –accessibility from standard PCs –parallel execution using threads

12. 12 EMBL Outstation — The European Bioinformatics Institute Future Development F Integration of further programs for sequence analysis F better integrity checks F better detection of redundancy F caching of program output

13. 13 EMBL Outstation — The European Bioinformatics Institute Credits SWISS-PROT F Amos Bairoch F Rolf Apweiler F Sergio Contrino F Wolfgang Fleischmann F Alain Gateau F Henning Hermjakob F Maria Martin F Steffen Möller Collaborators F Terri Attwood F Phil Scordis F Alex Bateman F Ewan Birney F Henrik Nielsen F Anders Krogh F Astrid Reinhard F Ulf Leser

14. 14 EMBL Outstation — The European Bioinformatics Institute Multilevel architecture F Specialisatio n F Easier maintenance

15. 15 EMBL Outstation — The European Bioinformatics Institute Framework: Analysers+Dispatchers F Bidirectional communication between Dispatchers:Determine Dataflow Analysers:Create Annotation