https://gydb.org/index.php?action=history&feed=atom&title=GPRO_Wiki GPRO Wiki - Revision history 2026-06-09T17:08:42Z Revision history for this page on the wiki MediaWiki 1.35.0 https://gydb.org/index.php?title=GPRO_Wiki&diff=1481&oldid=prev imported>Gydbwiki at 10:11, 22 May 2015 2015-05-22T10:11:08Z <p></p> <p><b>New page</b></p><div>&lt;p&gt;<br /> #[[Introduction and overview]]<br /> ##NGS bioinformatic analysis<br /> ##About GPRO<br /> ##Current version and further implementations&lt;/p&gt;&lt;p&gt;<br /> #[[Acquiring and installing GPRO]]<br /> ##Copyright and license<br /> ##System requirements<br /> ##Installation<br /> ##Warranty and technical support &lt;/p&gt;&lt;p&gt;<br /> #[[Software Layout and Computing Cluster]]<br /> ##Workbench and GUIs<br /> ##Computing cluster overview&lt;/p&gt;&lt;p&gt;<br /> #[[Mouse functions and tricks]]<br /> ##How to deal with GPRO depending on the GUI<br /> ##At the directory space<br /> ##About the database editor and fasta explorer<br /> ##Dealing with the worksheet<br /> ##FTP explorer and pipeline GUIs<br /> ##Working with management and data mining utilities&lt;/p&gt;&lt;p&gt;<br /> #[[The menu]]<br /> ##Tools and functions<br /> ###Databases<br /> ###Directory<br /> ###Editor<br /> ###Data preprocessing<br /> ###Functional analyses<br /> ###Alignment analyses<br /> ###Management<br /> ###Preferences<br /> ###Help&lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Editor]] <br /> ##Sequence editing<br /> ##Database editor<br /> ###Menu<br /> ####File<br /> ####Search and replace fasta labels <br /> ####Export and Remove seqs <br /> ####Find Motifs<br /> ####Undo<br /> ###Fasta Explorer<br /> ##TIME sequence editor<br /> ###Menu<br /> ####File<br /> ####Edit<br /> ####Translate <br /> ####Geometry<br /> ####Orientation<br /> ####Find ORFs<br /> ####Find motifs &lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Data preprocessing]]<br /> ##Data preprocessing<br /> ##Menu<br /> ###Converters<br /> ###Private user tools<br /> ###Processing and cleaning<br /> ###Quality analyses<br /> ##How to proceed<br /> &lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Functional analyses]]<br /> ##Functional analysis overview<br /> ##BLAST and HMM searches<br /> ###Format BLAST databases<br /> ###BLAST analyses <br /> ###HMM analyses<br /> ###Process BLAST outputs <br /> ###Process HMM outputs <br /> ##InterproScan <br /> ###Running INTERPROSCAN via GPRO<br /> ###Processing INTERPROSCAN outputs<br /> ##Augustus <br /> ###Running Augustus via GPRO&lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Alignment analysis]]<br /> ##Sequence Logos<br /> ##HMMs and consensus sequences&lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Management]]<br /> ##Management overview<br /> ##Files and folders<br /> ###Join folders<br /> ###Join files<br /> ####Select files and place them in a single folder <br /> ####Select XML files and place them in a single folder <br /> ####Join files in a single file <br /> ####Join XML files in a single XML file <br /> ###Split files<br /> ####Split files by sequence names<br /> ####Split files into blocks<br /> ##Find sequences <br /> ##Alignments<br /> ###Join alignments <br /> ###Format alignments&lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Preferences]]<br /> ##Pipeline connection settings<br /> ##Worksheet preferences<br /> ##Evidence code weights<br /> ##Activate/license softwares<br /> ##Proxy connection settings&lt;/p&gt;&lt;p&gt;<br /> #[[Menu Tools: Help]]<br /> ##About GPRO<br /> ##Manual<br /> ##Report suggestions and bugs<br /> ##Check updates&lt;/p&gt;&lt;p&gt;<br /> #[[Worksheet annotation system ( I )]]<br /> ##Managing annotation with the worksheet of GPRO: Multihit and Single hit CSV files<br /> ##Worksheet overview <br /> ##Worksheet menu: File Tab <br /> ###Open worksheet<br /> ###Save<br /> ###Save as<br /> ###Download GenBank Accession files<br /> ###Download sequences by GI<br /> ###Set as default worksheet<br /> ###Unset as default worksheet<br /> ###Import<br /> ####Append worksheet<br /> ####Combine worksheets<br /> ####Clusters<br /> ###Export<br /> ####Export worksheet and FASTA<br /> ####Export annotation file<br /> ####Export categories and clusters<br /> ###Show/Hide columns<br /> ##Workseet menu: File Tab <br /> ###Search and replace<br /> ###Undo<br /> ##Worksheet menu: Sorting/Filtering<br /> ###Sorting<br /> ###Filter by position&lt;/p&gt;&lt;p&gt;<br /> #[[Worksheet annotation system ( II )]]<br /> ##Worksheet menu: Annotation Tab<br /> ###GO annotation<br /> ####Append GO terms<br /> ####Evidende code weights<br /> ####Display graph<br /> ####GO depth statistics<br /> ###Append InterPro data<br /> ###Append COG/KOG terms<br /> ###Apply annotation colors<br /> ###Switch database IDs<br /> ##Worksheet menu: Select Tab <br /> ###Select sequences by key terms<br /> ###Select sequences by expect or statistics values<br /> ###Selecting set of sequences differentiated by colors<br /> ###Selecting sequences by multiple criteria<br /> ###Delete checked sequences from the Worksheet<br /> ##Worksheet menu: Associate database <br /> ###Associate fasta sequences to your annotation CSV file<br /> ###Remove association between your fasta file and the CSV<br /> ##Worksheet menu: Statistics <br /> ###Numerical data statistics<br /> ###Categorical data statistics<br /> ##Worksheet menu: Metabolic pathways<br /> ##Worksheet menu:Transcriptome post-processing<br /> ###Filter best isoform<br /> ###Sequence trimming&lt;/p&gt;&lt;p&gt;<br /> #[[Acknowledgements and citing]]<br /> ##Acknowledgements<br /> ##Citing the last GPRO version&lt;/p&gt;<br /> <br /> [[Category:GPRO manual]]</div> imported>Gydbwiki