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ORFer Home
General
Howto
Menus
Search failed
Set the preferences
Search for a single sequence
Search for a list of sequences
Sort data
Set preferences
Local database setup
Save sequences as Fasta files
Save sequences as tabulator delimited files
Store sequences in a local database
Retrieve sequences from the local database
Copy/paste data from ORFer to other applications
Use ORFer in non-interactive mode
Search GI or Accession
Open Search List
Get all Sequences in local database
Clear search list
Repeat Search
Abort search
Reset
Exit Program
Save Fasta Protein
Save Fasta DNA
Save to local database
Save Tab delimited
Save selected only
Show messages
Show errors
About
In the Search menu, choose Search GI or Accession. Enter a GI identifier (a number) or an accession number. Numbers will be interpreted as GI identifiers and entries containing letters will be interpreted as text.
Prepare a text file with one GI identifier or accession number per line. Go to the Search menu and choose Open Search List. Select the file you have prepared. ORFer will start searching for the sequences in the file immediately.
Click on the header of column to sort by in ascending order. Click again to sort in descending order.
If you use Java Web Start, preferences will be stored somewhere in the Java Web Start directory. Otherwise, a file orfer.properties will be generated in the directory that ORFer was started in.
The Preferences can be used to adjust the way ORFer does the searching.
NCBI XML sequence files often contain more than one sequence entry. Choose Retrieve only exact match, if you want the exact sequence that was searched only, otherwise choose Retrieve all sequences in XML files.
If there are sequences stored in the local database, choose Search in local database first. ORFer will try to get the sequences from the local database, which saves time and bandwidth.
Validate XML against .dtd files - this is not recommended because it is very slow and causes extra network traffic.
Use local XML files: XML files retrieved from NCBI can be stored in a local folder and reused later. Saves time and bandwidth.
The Preferences are also used to set the local database connection.
To store sequences in a local database, prepare a MySQL, MS Access or Oracle Database and enter your database parameters in the ORFer preferences. Use the drop down menu Select URL template for ... to quickly generate a URL string for your type of database.
Saving the password is not recommended in the current version, because the password will be saved without encryption in the orfer.properties file.
First of all you'll have to make the database:
mysql < orfer_mysql.sql to create the necessary
objects in an MySQL database.
You can copy data from the Search Results or Search List tables and paste the data to other applications. Use the right mouse button to open the copy/select pop-up menu. (Thanks to the SQuirrel-SQL project for the code of the pop-up menu). You can paste multiple (or all) fields in the table to Excel. With Linux, use xclipboard to get hold of the data that was copied.
ORFer will save all protein or DNA sequences to one Fasta file, if you choose Save Fasta Protein or Save Fasta DNA in the Save menu. If you want to save only a set of sequences, check the boxes in the Selected column in the Search Results table of those sequences and select Save selected only in the Save menu.
This format is suited for opening with Microsoft Excel. Open the Save menu and choose Save Tab delimited. By default, all sequences are saved. If you want to save only a set of sequences, check the boxes in the Selected column in the Search Results table of those sequences and select Save selected only in the Save menu.
Set up the local database as described. If you choose not to save the database password, make sure to enter it again upon program start. By default, all sequences are saved. If you want to save only a set of sequences, check the boxes in the Selected column in the Search Results table of those sequences and select Save selected only in the Save menu.
Open the Search menu and choose Get all sequences in local database. This will read all entries present in the local database. If you want to retrieve a subset of entries, prepare a list of the respective GIs. Select Search in local database first in the Preferences, open the Search menu and select your list file by choosing Open Search List.
If you are using Oracle or mySQL, you could use SQuirrel-SQL to retrieve a list of GI identifiers by SQL.
With the help menu, you can open text boxes with success messages (Show messages) and error messages (Show errors). This is mainly useful if something goes wrong.
ORFer can be run in non-interactive mode by excuting orfer.jar from the command
line with a the file name of list of GI identifier or accession numbers as argument.
orfer.jar is included in the file orfer-x.x-bin.zip, which can be downloaded
at SourceForge
java -jar orfer.jar gi_liste.txt
All protein and DNA sequences will be written to the files pep.fasta
and dna.fasta in the local directory, respectively.
Place a file orfer.properties with
the details of the database connection in the same directory. All retrieved
sequences are automatically stored in the local database.
Clear search list
Repeat Search
Abort search
Reset
Exit Program
Sorry, not all menu commands are documented yet.
Search might fail for certain sequences. Some of the XML files sent by the NCBI are malformed and cannot be parsed by ORFer. The reason could also be an interrupted internet connection or a high load on the NCBI web server. If an accession number was used to search, the search should be repeated with the respective GI identifier. To convert a list of accession numbers to GI identifiers, use NCBI Batch Entrez: upload the list of accession number and choose GI list as the save format.
It might be helpful to display general output and error messages on a Java console window. To display the Java console, set the appropriate options in the Java Web Start Application Manager in Files/Preferences/Advanced.