Retrogenomics WWU Muenster
About Tools Intern
Usage of GPAC
The usage of this tool is easy: You just need an internet browser and enter the request data into the provided page and then submit the data to the server, which can be displayed when results are available. You don't have to keep the browser open, you can do any other task and come back later again.
A few word about browsers. The tested and best working browsers are firefox, chromium and opera. Internet Explorer is working with newer version. Safari is known for having problems after selecting rows and redisplay the content.

Enter Request Data

The first step is to enter the input (request) data. Click on "Start Application" in the left menu. It appears a screen
input
Id The number (identification) of the request already started. Note: When opening the input mask the first time after starting the browser, the selection box right from this field is (automatically) validated against the ids on the server.
Target The species against which the data is calculated.
Title The title which appears later on on top of the output table. If not entered the actual date and hours is taken and appended by the request id.
Reference genome coordinates The request input data
File The request input data - but taken from a (local) file of your computer.
Species The species of interest. These fields coresponds to the selected target!
Here can can enter the request data. There are three ways to proceed: either you (only) type the id of an already made request, select a row in "Select one of the last requests..." (where the last 10 runs are stored locally) or you fill the input fields of a new request, below the id line. E.g. if you select a target (hg19) then the species are added and you can proceed.

Select a Target

If you select a target, the species for that target are added to be selected.
input

Select RepeatMasker Input

Or you can select a RepeatMasker file. When doing so, the file is analyzed (locally on your browser / computer) and the found families are displayed.
input
Select at least one family of interest and the coodinates textfiled will be filled witht that RepeatMasker data with the appropriate selected families.

Notes

The button "Testcase" just enteres data for a test run. Clicking on "OK" will send that data. For resetting the mask click on "Start Application" on the left menu.

Limits

  • The size of the input data must not exceed 32MB and the row number must be less than 100000. The maximum filsize is 512MB - but note, that selecting/sending big data can result in long waits or browser freeze.
  • The displayed amout of lines in the result table depends of the number of displayed cells - the maximum is set actuallay to 200000. This is done, because many browsers have problems handling much bigger data.
  • The request and result is available for 28 days on the server. After that time it will be deleted.

Input Data Format

The input data consists of a text file with lines of the form
"chr" nr BLANKS start BLANKS end [BLANKS info]
or
"chr" nr ":" start "-" end [BLANKS info]
where BLANKS are single or multiple blanks or tabulators, nr is the number of the chromosom, start is the start position, end is the end position and info is a textual information.
Example
chr22 39644734 39644831 human5SrRNA_chr22_edit_39644734_39644831_+_perfect
chr22 26111046 26111136 human5SrRNA_chr22_edit_26111046_26111136_C_perfect
chr22 31701390 31701479 human5SrRNA_chr22_edit_31701390_31701479_+_perfect
chr22 33816271 33816312 human5SrRNA_chr22_edit_33816271_33816312_C_perfect
or
chr22:39644734-39644831
chr22:26111046-26111136 human5SrRNA_chr22_edit_26111046_26111136_C_perfect
chr22:31701390-31701479 human5SrRNA_chr22_edit_31701390_31701479_+_perfect
chr22:33816271-33816312

If you submit data, but some lines are incorrect, only the valid lines are send to calculation. You can either go back direct from here with the invalid data to the input mask or later when the request is finished. Invalid lines are marked by a comment "#" at the start and they are skipped for calculation.

Start Calculation

After submitting the request, following screen appears
waiting
The request is put in a queue and will be calculated in order of arrival. It means: closing the browser and opening it again does not stop the calculation! You have to either bookmark the link, write down the id of the request or (if you dont want to do), just go to "Start Application" and select the last row under "Select one of the last requests...". As long as the request is not ready, following mask will be displayed
waiting-2
You can stay on this page and wait. See the note, that this page is updated every 60 seconds. Click on "Check manually" breaks this time and immediately checks if the result is available.

Display Data

If the request is ready calculated following screen appears
result

Sort Table

This table offers sorting (by quality or by species/columns), which is done on the local computer (not on the server).

By Quality (+, -, ++, --)

First: sorting offered by the menu on the left side: The option "+" sorts the rows by counting the number of "++", "+", "+-" and "+(/)" found in rows. The option "-" sorts by counting "-" and "-(=)". The option "++" sorts only by counting the number of "++", where "--" sorts only by counting the number of "--".

By Columns

Second: Sorting by columns is done by clicking on the column header. The first selected header is (re-)ordered to the left of the table and so on - so you can see the order of seltion critaria. The first 3 columns stay in the order, although you can sort by "info" and "region". The column sorting uses the symbols in the species columns as the criteria for sorting. Note: The hit coordinate is allways implicitly added as the last sort critaria to make the sort stable.

Manually

Despite the sorting by column or by "+" or "-", you may place rows in your preferred order. "Cut Selected", "Paste Before" and "Paste After" gives you the possibility to move rows to other places in the table. Note: This sorting is temporary and lost if you click on any column or sorting button!

Select Rows

Rows are selected (and also deselected) by clicking on the selection box in the first column of each line. Ranges of rows are selected by keeping the shift key pressed and select first and last row of the selected area. See also "Cut Selected", "Paste Before" and "Paste After" (already mentioned in "Manually"). Additionally to this seletion mechanism, there are two special ones:

Display Perfect

(Re-)displays the table, but only for rows, where the species have only "+" or "-" as symbols.

Display Selected

(Re-)displays the table only for the selected rows.

Operations

Recalculate Valid Data

Take the (valid) input data and settings of this result, fill and redisplay the input mask. This gives the opportunity to start a new calculation with modified input.

Calculate Errors

Take the invalid input data and already made settings of the request, fill and redisplay the input mask. This gives the opportunity to continue with calculation of the missing invalid data.

Display Symbols

Display the meaning of symbols used in the result table in a separate window.

Export to Excel

Exports the values of the displayed result table direct into Excel, Libre- and OpenOffice or to store the data into a file that can be loaded with that named programs.

Print Result

To print the result table the best is to click on "Print" in the left menu (not any other printer symbol!). The table will be redisplyed in a new window or tab, but without any uneccesary information and some recoloring - so it can be printed as a whole. To Click on "Print..." in the browser top menu or press CTRL-P for "direct" printing from the browser may print only a part of the result table.
print

Display Tree

Opens a new window and displays the textual representation of the marker tree in newick format and below the graphical view. Another option of displaying newick trees is here.
markertree

Reset

Restores the table to the initial state.