imported>Gydbwiki at 14:17, 1 April 2015

2015-04-01T14:17:50Z

New page

[[GPRO_Wiki|Return to Index]]

=The Menu=

== Tools and functions ==

GPRO implements a central main MENU (Figure 5.1) horizontally located at the top of the software layout and that integrates the following tabs:

[[File:gp_5_1.jpg|800px]]

<table style="width:800px">
<tr>
<td>'''Figure 5.1'''. Menu and functions.
</td>
</tr>
</table>
 

There follows a description of each tab according to the numbers highlighted below figure

=== 1.- Databases ===
 
This tab implements five utiliies:

*'''Select directory folder''': for selecting a folder as a directory workspace.
*'''Open single FASTA file''': to open sequence and database files in fasta format from any site of your PC.
*'''GenBank Accession''': to retrieve GenBank sequence accessions from GenBank at [http://www.ncbi.nlm.nih.gov/ NCBI].
*'''Open worksheet''': to open annotation worksheet files which are CSV files (plain files with comma-separated values).
*'''New worksheet''': To create a new empty worksheet.

=== 2.- Directory ===

 
Using this tab, users can show or hide the directory at the left of the tool GUI

=== 3.- Editor ===

 
This tab gives the option to launch two editors.

The first is a [[Menu Tools: Editor | "Database editor"]] associated to the worksheet and implemented with distinct utilities of editing, mining and management of plain fasta files.

The second is an implementation of [[Menu Tools: Editor | "TIME editor"]] an editor/analyzer of sequences of up to two gigabases

=== 4.- Data preprocessing===

 
This tab gives you access to the GUI of a pipeline of [[Menu Tools: Data preprocessing | "Preprocessing tools" ]] for quality analysis and data preprocessing installed in the computing cluster with which you can configure and design ad hoc a particular analysis flowchart based on distinct tools.

===5.- Functional analyses ===

 
This tab allows launching of GUIs for three distinct functional analysis tools installed in the remote cluster server:
One is a [[Menu Tools: BLAST and HMM Pipeline | "BLAST and HMM search Pipeline plus GO-annotation"]]
The other is a [[Menu Tools: INTERPROSCAN Pipeline | "pipeline for INTERPRO based annotation"]]
The third is a server for de novo gene finding based on [[Menu Tools: Augustus Server | "Augustus software"]]

=== 6.- Alignment analyses ===

 
This tab implements two GUIs for multiple alignment tools:

One is for run a [[Menu Tools: Sequence Logos | "Sequence Logos maker"]] based on multiple alignment inputs.

The second lets to launch a HMMER server installed in the computing cluster for creating [[Menu Tools: HMMs and Consensus Sequences | "HMM profiles and MRC sequences"]]

===7.- Management ===

 
The tab [[Menu Tools: Management | "Management"]] launches a suite of scripts to manage files and folders in various ways. For instance, users can join, split and rearrange files, folders and contents. In addition, users can execute specific data mining searches in these files and folders, and export the results in new files and folders.

===8.- Preferences ===

 
The tab [[Menu Tools: Preferences | "Preferences"]] is useful for fixing the with regards to diverse issues (for example, FTP and pipeline connection).

===9.- Help ===

 
The tab [[Menu Tools: Help | "help"]] is for accessing the technical support service, the user guide (this wiki) and intrinsic information of GPRO.

[[GPRO_Wiki|Return to Index]]

[[Category:GPRO manual]]

The menu - Revision history

imported>Gydbwiki at 14:17, 1 April 2015