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Sequence Extraction

Extract sequences from alignment files based on sequence IDs or regular expression.

Steps​

  1. Select the Sequences button from the navigation bar.
  2. Select Extract sequences from the dropdown menu.
  3. Add the input files by clicking the Add file button. On desktop platforms, you can also input a directory by clicking the Add directory button. The app will look for matching files in the directory.
  4. All the input files will be displayed in the input tab bar. You can remove the file by clicking the Remove button. Removing the file will only remove it from input list and not from the file system.
  5. Select input format (optional). See the supported file extensions for the list of supported extensions for alignment files.
  6. Add extraction parameters.
  7. Add the output directory by clicking the Add output directory button. On mobile platforms, the directory will be the default directory for the app.
  8. Click the Run button labeled Extract to start the task.
  9. Share the output (optional).

Parameters​

The app allows you to extract sequences based on the following parameters:

Input ID in a file​

The app allows you to input a file containing sequence IDs to extract. The app will use the file to match the sequence ID. The file should be in plain text format. Each line should contain one sequence ID.

seq1
seq2
seq3

Input semi-colon separated IDs​

The app will use the sequence IDs to match the sequence ID.

seq1;seq2;seq3

Write regular expression​

The regular expression will be used to match the sequence ID. The syntax for the regular expression follows the Rust regex syntax. You can use regex101 to test your regular expression.

Example:

  • ^seq[0-9]+ will match all sequence ID that starts with seq followed by one or more numbers.
  • ^seq[0-9]{2} will match all sequence ID that starts with seq followed by exactly two numbers.
  • ^rattus will match all sequence ID that starts with rattus.

Output file​

All matched sequences will be extracted from each input file. The app will create a new file for each input file. For example, if theSet the format in output section to determine the output format.