Sequence Analysis
FASTA Cleanup
Tidy pasted FASTA: strip junk, wrap, name and number records, gaps kept.
An example is loaded. Click here and it clears.
Examples:
Settings
Tidied
- Records
- 5
- Total length
- 119
- Characters removed
- 1
- Names generated
- 1
- Duplicates numbered
- 1
- Empty records dropped
- 1
| Name | Length | Status |
|---|---|---|
| sequence | 20 | name generated |
| clone_1 first pick | 39 | unchanged |
| clone_1 second pick from the same plate | 20 | unchanged |
| clone_2 backup | 20 | unchanged |
| clone_2 backup_2 | 20 | duplicate (numbered) |
The tidied text is ready to paste into the alignment tool.
How to use it
- Paste whatever you have: a FASTA file, a block with position numbers down the margin, or a bare sequence.
- Set the wrap width and the case. Leave the gap box ticked if this came from an alignment.
- Read the counters, check the per-record table, then copy or download the tidied file.
Worth knowing
- Gaps are kept by default. Removing them from an alignment leaves rows that still look like sequences and no longer line up with each other, and nothing downstream would notice.
- Duplicate identifiers are numbered rather than left alone, because a program that keys on the name will otherwise keep one record and quietly drop the other.
- Amino acids survive. A cleaner that only knows nucleotide codes deletes E, F, I, L, P and Q out of a protein sequence and reports it as tidying.
Questions
Anything that is not a sequence letter or a gap. Spaces, line breaks and the position numbers some viewers print down the margin are not counted, because those are layout rather than something anybody typed.
A header with no sequence under it is dropped and counted separately. If a record vanished, the counter for empty records is where it went.
The first word of the header line. The rest is kept as a description and travels with the record.
The other sequence tools
- Multiple Sequence Alignment — Align a family of sequences and read the conserved columns.
- GC Content Calculator — GC and AT content, skew, and GC along the sequence.
- DNA to Protein Translation — Six-frame translation and open reading frames, in any NCBI genetic code.