RFLP Identification tool for Armillaria species:
Description of the user graphical interface
Requirements:
System: Windows® 95, Windows® 98, Windows® 2000, Windows® XP
Additional: Microsoft® Word
Best viewed at: 1152 x 864 pixels, 32 bit colour
Download description file (pdf)
General menu:
The General (start) menu gives the five options:
- Analysis: RFLP profile analysis function of the application.
- Add data: RFLP profiles, enzymes or references can be added, edited or removed from the database.
- List all RFLP profiles: IGS-1 or ITS RFLP profiles are listed from the database and can be printed to a Microsoft® Word file.
- References: Lists all references from the database and exports references to a Microsoft® Word file if required.
- Exit: Exits the program.
Analysis window
User RFLP profiles are analysed by following the steps outlined below:
1) ITS or IGS-1 rDNA region is selected by moving the mouse-pointer over the required region. The activated region change colours when selected.
2) A primer-pair is selected by moving the mouse-pointer over one of the primer-pairs; change in colour indicates the selected primer-pair.
3) Choosing primer pair P-1 / 5S2B will activate options for the PCR fragment size of the African A. fuscipes (> 1000 bp.) or A. heimii (< 1000 bp.).
4) An enzyme is selected from a drop-down menu that lists all enzymes and their restriction sequences from the database.
5) The number of fragments (between 1 and 5) to be entered are selected from a drop-down menu.
6) Boxes for the fragment sizes of the RFLP profile open after Step 4. Only fragment sizes between 50 and 700 bp. are accepted.
7) The Analyze button is pressed to execute the analysis.
One of two analysis algorithms, sum of differences and normal distribution error, can be selected by the user for the analysis.
Analysis result window
The Result window gives a list of species, in the order of the best to the worst match with the user RFLP profile, together with all their information. Detailed information pertaining to a specific species record (name, full reference, PCR region, primer pairs, PCR fragment sizes, enzyme used, number of fragments and fragment sizes) is displayed after selecting the record from the table. The table can also be exported to a Microsoft® Word file using the Print button. The Back button will take the user to the analysis window, which will still contain all the selected and entered data; these can be changed and the analysis repeated. The Exit button returns the user to the General window.
Add data – RFLP Profile window
RFLP profile records can be added, updated or deleted within the Add Data window after pressing the RFLP Profile button. This procedure requires the following steps:
1) A list of all records within the database is displayed in a table.
2) A specific record can be selected with the mouse-pointer by clicking on any of the items in the table; this will highlight the selection and show detailed information regarding the species.
3) The selected record can then be updated or deleted using the Update and Delete buttons.
New RFLP profiles are added to the database by pressing the New button (see screen on previous page).
1) Data are entered by the user or selected from pull-down-menus.
2) The Add button will add the data to the database and the next record can then be entered.
3) The Done button will close the Add function and the new records are displayed in the table.
The procedure outlined above is also applicable to adding, updating and removing enzymes and reference records.
List all profiles window
Selected subsets of RFLP profiles can be displayed following the steps outlined below:
1) An rDNA region is selected using the IGS or ITS buttons.
2) A table with all records in the database pertaining to that region is displayed.
3) A specific record can be selected from the database in the table.
4) The Selected record is highlighted and detailed information is displayed.
5) A list of all the records in the database pertaining to the selected rDNA region can be exported to Microsoft® Word using the Print button.
6) The Exit button returns the user to the General window.
List all references window
References stored in the database are viewed through the following steps:
1) A table with all records in the database is displayed.
2) A specific record can be selected from the database.
3) The selected record is highlighted and detailed information is displayed.
4) A list of all the reference records can be exported to Microsoft® Word using the Print button.
5) The Exit button returns the user to the General window.
