Server : pat.cbsrs.fr Publication : Gracy et al. (2005) Nucleic Acids Res. (33) W65.

1. PATProtein Analysis toolkit Integrated biocomputing server: - 76 tools dedicated to protein analysis - Standardized web interface - Interactive tool combination - Web session manager - Macro language for complex analysis - Evolutive modular architecture Example of non globular structural prediction. Server: http://pat.cbs.cnrs.fr Publication: Gracy et al. (2005) Nucleic Acids Res. (33) W65.

2. PATProtein Analysis toolkit Input and output formats are automatically recognized: • User does not need to bother with data format conversions. • Tools can be combined “on the fly”, output data of the first tool is automatically converted to the input format required by the second tool. Tools can be interactively combined : • Parallel and serial combinations are allowed. • “Parallelizable” tools are listed in the parallel section of the form. • “Pipelinable” tools are listed in the “Output redirection” popup menus. - When a pipeline is activated, web forms are dynamically expanded and new tool options proposed.

3. PATProtein Analysis toolkit Processing flowchart: 1. Input format is automatically guessed. 2. Input data parsing or index-based database search. 3. Input data is converted to the format required by analysis tool. 4. Web form parameters are translated into an executable script. 5. Script processing results are stored and maintained by web session manager.

4. PATProtein Analysis toolkit Session manager: • - Each job launched during a web session is accessible from an user-specific output table. • Complex analyses obtained by tool combination are decomposed into elementary steps whose intermediate results are accessible from the output table. • - All input, tools, output and possible redirections are one-click away from this centralized table.

5. PATProtein Analysis toolkit • Simple but powerful macro language. • Parallel and pipeline tool combinations are translated into macros which are accessible from the “Macro” button for repetitive use of complex queries. • Macro examples: • Macro 1: "wublast2 -d nrl3d | cdhit | clustalw | mview“. • This macro searches query similarities in the database NRL3D using WUBLAST2, selects representative homologs with CDHIT, aligns them with CLUSTALW, then displays the resulting multiple alignment using MVIEW. • Macro 2: "psiblast -d uniprot -j 3 | cdhit | clustalw | map dsc on -seg | major 2d | selex". This macro searches query similarities in the database UNIPROT using 3 iterations of PSI-BLAST, selects representative homologs among them with CDHIT, aligns their sequences using CLUSTALW, predicts their secondary structure with DSC, build a consensus prediction and finally prints all the predictions using the SELEX format. • - Macro 3: "dsc, predator, psipred, tmpred, tmap, seg, ncoils | major 2d, major mm | msf". This macro launches different local structure prediction tools, then computes a majority prediction from secondary structure predictions (major 2d) and transmembrane segment predictions (major mm), then prints the resulting output following the MSF format.