Sequence Gap Cleaner

Remove or preserve gaps, spaces, numbers, and special characters from sequences

What is Sequence Gap Cleaner?

Sequence Gap Cleaner is a tool that removes unwanted characters from DNA, RNA, or protein sequences. It can remove spaces, alignment gaps (- and .), numbers, and line breaks while preserving FASTA headers. This is essential when cleaning sequences from alignment files, formatted text, or when preparing sequences for analysis tools that don't accept special characters.

How to Use This Gap Cleaner

Quick guide to clean your sequences:

  1. Select which characters to remove (spaces, gaps, numbers, line breaks)
  2. Paste your sequence with unwanted characters
  3. Results appear automatically with cleaned sequence
  4. Download or copy the cleaned output

When to Use

This tool is useful when you need to:

  • Remove gaps from multiple sequence alignments
  • Clean sequences copied from formatted documents
  • Remove numbering from sequences
  • Prepare sequences for tools that don't accept special characters
  • Convert aligned sequences back to plain format

Example Input

Sample sequence with gaps and spaces:

ATC GAT CGA---TCG ATC...GAT 123 456 789

Contains spaces, gaps (- and .), and numbers.

Example Output

Cleaned sequence:

ATCGATCGATCGATCGAT

All spaces, gaps, and numbers removed.

FAQ

Q: Does this preserve FASTA headers?
A: Yes, FASTA headers (lines starting with >) are always preserved.

Q: What characters count as gaps?
A: The tool removes hyphens (-) and periods (.) which are standard gap characters in alignments.

Q: Can I keep line breaks?
A: Yes, uncheck "Remove line breaks" to preserve original formatting.