Sequence Extraction

Desktop

ABCDE

Phone

ABCDE

• ASequences tab
• BTool switcher
• CInput files
• DRun button
• EFile panel

New interface coming soon

This page shows the new SEGUI interface, which is in development. The current release (v1.1.3) looks different, and features marked In development are not available in it yet.

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

Steps

1. Select Sequences in the navigation bar A.
2. Open Extract sequences from the tool list on wide windows, or select the tool name B at the top of the page to switch tools.
3. Add the input files C with Browse files, Browse folder, or Open archive. SEGUI searches a folder and its subfolders for files that match the tool's input format. See file input for mobile options.
4. The Input tab of the file panel E lists the input files. On phones and narrow windows, open it with the files button next to the tool name. To remove files from the list, choose Select, pick the files, and select Remove. The files stay on your device.
5. Select input format (optional). See the supported file extensions for the list of supported extensions for alignment files.
6. Add extraction parameters.
7. Select Browse under Select output directory to choose the output folder. On phones and tablets, enter a Directory name instead; SEGUI saves it in the app's own folder.
8. Select the run button D, labeled Extract, to start the task.
9. Export or share the output (optional). See exporting output.

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.