FASTA Deduplicator

Remove duplicate sequences from FASTA files by sequence content or headers. Clean your sequence databases efficiently.

Deduplication Statistics

Original
0
Unique
0
Removed
0
Reduction
0%

What is FASTA Deduplicator?

This tool removes duplicate sequences from FASTA files based on either sequence content or header IDs. Essential for cleaning sequence databases, removing redundancy, and preparing unique datasets for analysis.

How to Use This Tool

  1. Paste or upload FASTA sequences
  2. Choose deduplication mode (by sequence or header)
  3. Select case sensitivity and occurrence preference
  4. Download cleaned, unique sequences

When to Use

  • Cleaning sequence databases
  • Removing PCR duplicates
  • Preparing non-redundant datasets
  • Merging multiple FASTA files

Deduplication Modes

By Sequence: Removes identical sequences regardless of headers

By Header: Removes duplicate IDs keeping unique sequences

Case Sensitive: Treats ATCG differently from atcg

Example Dataset

>Gene1
ATCGATCG
>Gene2_duplicate
ATCGATCG
>Gene3
GCTAGCTA

Results in 2 unique sequences.

FAQ

Q: Which duplicate is kept?
A: By default, the first occurrence. Uncheck "Keep first" for last.

Q: Does it preserve FASTA formatting?
A: Yes, headers and sequences are maintained.