These sequence repeats, usually with no biological consequences, have been used for many years as 'markers' that can identify specific points in the genome.

The SSR Extractor utility finds simple sequence repeats within DNA sequences and displays them in a table. The table is interactive and supports filtering, sorting, data re-processing and exporting to CSV format (Excel).

• Click the Browse button and select a Fasta file from your local drive
• Alternatively, enter the local Fasta file path directly
• Note: Do not use files larger than 1Mb
• Set processing parameters
  • Unit length: The length of the substring that is repeated
    e.g. for unit length = 3, the SSR unit can be AAT, CGA etc.
    and the complete SSR can be AATAAT, CGACGACGA etc.
  • Minimum length: Minmium length (in nucleotides) of complete SSR
    e.g. for unit length = 3 and minimum length = 15
    the SSR unit must be repeated at least five times
  • Primer Min: Minimum distance of SSR from either edge of sequence
    Required for primer definition to be used in PCR processing
  • Primer Max: Desired size of primer on either side of SSR
    This value sets the desired primer length
    Primer Min. sets the minimum primer length
• Click the Import File button
  • The selected file will be loaded
  • The loaded data will be searched for SSRs according to the specified parameters
• Wait until a notifying message and the output table are displayed
  • This stage might take some time. The main time consuming element of the process is the file upload, which is extremely slow even on fast Internet connections (fast for downloads but not for uploads). Therefore it is not recommended to use this utility with large files.
  • When processing is complete a message will be displayed, showing processing information. Click the Hide Message to remove it.
  • The output table is displayed, showing the SSR sequences data.
• Proceed with one of the following:
  • Re-process same file by selecting new search parameters
    Modify any of the SSR search settings (Unit length, minimum length, primer length) and hit the Re-Process button.
  • Modify the table by setting filter and sort parameters and clicking the Update button
    See description of filter and sort parameters below
  • Export the table to Excel in CSV format
    See description below
  • Load a new file
    Click the Browse button and load another file

Re-process current (already loaded) file

• Process current SSRs
  Set filter/sort parameters (Accession, Start, Length, SSR unit, Sort fields, Sort directions) for the current SSRs, and click Update button
• Find new SSRs
  Find a new set of SSRs from the same file by selecting new search parameters (Unit length, minimum lenth, priner length) and hit the Re-Process button

Filter / sort the data
Select filter and sort parameters and click Update button
The first row sets data filtering parameters
The second row sets data sorting parameters

• Set Filter parameters
  • Accession: Filter data by Accession (ID)
  • Start >: Filter data by SSR location in the sequence
    Show only SSRs starting at or after specified location
  • Length >: Filter data by SSR length
    Show only SSRs equal to or larger than the specified value
  • SSR Unit: Filter data by SSR unit
    Show only SSRs made of repetitions of the specified base unit
• Set Sort parameters
  • Sort I: Sort data by the selected field
    This is the primary sorting field
  • Direction: Sorting direction for Sort I field
    Select either Ascending or Descending
  • Sort II: Sort data by Sort I and Sort II
    This is the secondary sorting field
  • Direction: Sorting direction for Sort II field
    Select either Ascending or Descending
• Click Update button to update the table according to specified filtering and sorting parameters
• Click the Reset button to restore table to the default paramaters

Save to Excel file (CSV)

• The user is prompted to save the current table to a CSV file on the local computer.
• The program suggests the input file name with a csv extension. This name can be modified to reflect the current settings.
• On Windows system with Excel installed, double-clicking a CSV files opens it in Excel.

• Context sensitive help:
  Placing the cursor over any label or button displays a help tooltip
• Input file size
  Uploading files over the Internet is slow even on fast connections. Avoid loading files larger than 1MB. Larger sizes can also be used, but they should better be split into smaller files.