GPRO Wiki

1. Introduction and overview
   1. NGS bioinformatic analysis
   2. About GPRO
   3. Current version and further implementations

2. Acquiring and installing GPRO
   1. Copyright and license
   2. System requirements
   3. Installation
   4. Warranty and technical support

3. Software Layout and Computing Cluster
   1. Workbench and GUIs
   2. Computing cluster overview

4. Mouse functions and tricks
   1. How to deal with GPRO depending on the GUI
   2. At the directory space
   3. About the database editor and fasta explorer
   4. Dealing with the worksheet
   5. FTP explorer and pipeline GUIs
   6. Working with management and data mining utilities

5. The menu
   1. Tools and functions
      1. Databases
      2. Directory
      3. Editor
      4. Data preprocessing
      5. Functional analyses
      6. Alignment analyses
      7. Management
      8. Preferences
      9. Help

6. Menu Tools: Editor
   1. Sequence editing
   2. Database editor
      1. Menu
         1. File
         2. Search and replace fasta labels
         3. Export and Remove seqs
         4. Find Motifs
         5. Undo
      2. Fasta Explorer
   3. TIME sequence editor
      1. Menu
         1. File
         2. Edit
         3. Translate
         4. Geometry
         5. Orientation
         6. Find ORFs
         7. Find motifs

7. Menu Tools: Data preprocessing
   1. Data preprocessing
   2. Menu
      1. Converters
      2. Private user tools
      3. Processing and cleaning
      4. Quality analyses
   3. How to proceed

1. Menu Tools: Functional analyses
   1. Functional analysis overview
   2. BLAST and HMM searches
      1. Format BLAST databases
      2. BLAST analyses
      3. HMM analyses
      4. Process BLAST outputs
      5. Process HMM outputs
   3. InterproScan
      1. Running INTERPROSCAN via GPRO
      2. Processing INTERPROSCAN outputs
   4. Augustus
      1. Running Augustus via GPRO

2. Menu Tools: Alignment analysis
   1. Sequence Logos
   2. HMMs and consensus sequences

3. Menu Tools: Management
   1. Management overview
   2. Files and folders
      1. Join folders
      2. Join files
         1. Select files and place them in a single folder
         2. Select XML files and place them in a single folder
         3. Join files in a single file
         4. Join XML files in a single XML file
      3. Split files
         1. Split files by sequence names
         2. Split files into blocks
   3. Find sequences
   4. Alignments
      1. Join alignments
      2. Format alignments

4. Menu Tools: Preferences
   1. Pipeline connection settings
   2. Worksheet preferences
   3. Evidence code weights
   4. Activate/license softwares
   5. Proxy connection settings

5. Menu Tools: Help
   1. About GPRO
   2. Manual
   3. Report suggestions and bugs
   4. Check updates

6. Worksheet annotation system ( I )
   1. Managing annotation with the worksheet of GPRO: Multihit and Single hit CSV files
   2. Worksheet overview
   3. Worksheet menu: File Tab
      1. Open worksheet
      2. Save
      3. Save as
      4. Download GenBank Accession files
      5. Download sequences by GI
      6. Set as default worksheet
      7. Unset as default worksheet
      8. Import
         1. Append worksheet
         2. Combine worksheets
         3. Clusters
      9. Export
         1. Export worksheet and FASTA
         2. Export annotation file
         3. Export categories and clusters
      10. Show/Hide columns
   4. Workseet menu: File Tab
      1. Search and replace
      2. Undo
   5. Worksheet menu: Sorting/Filtering
      1. Sorting
      2. Filter by position

7. Worksheet annotation system ( II )
   1. Worksheet menu: Annotation Tab
      1. GO annotation
         1. Append GO terms
         2. Evidende code weights
         3. Display graph
         4. GO depth statistics
      2. Append InterPro data
      3. Append COG/KOG terms
      4. Apply annotation colors
      5. Switch database IDs
   2. Worksheet menu: Select Tab
      1. Select sequences by key terms
      2. Select sequences by expect or statistics values
      3. Selecting set of sequences differentiated by colors
      4. Selecting sequences by multiple criteria
      5. Delete checked sequences from the Worksheet
   3. Worksheet menu: Associate database
      1. Associate fasta sequences to your annotation CSV file
      2. Remove association between your fasta file and the CSV
   4. Worksheet menu: Statistics
      1. Numerical data statistics
      2. Categorical data statistics
   5. Worksheet menu: Metabolic pathways
   6. Worksheet menu:Transcriptome post-processing
      1. Filter best isoform
      2. Sequence trimming

8. Acknowledgements and citing
   1. Acknowledgements
   2. Citing the last GPRO version