Sequence Analysis
GC Content Calculator
GC and AT content, base composition, skew, and GC along the sequence.
An example is loaded. Click here and it clears.
Examples:
sequence
- Length
- 300
- GC content
- 46.0 %
- AT content
- 54.0 %
- GC skew
- 0.159
- AT skew
- 0.000
Base composition
- G 80 (26.7 %)
- C 58 (19.3 %)
- A 81 (27.0 %)
- T 81 (27.0 %)
GC along the sequence (50 nt window)
How to use it
- Paste a sequence, a FASTA record, or several records at once.
- Set the window size. It decides how much detail the GC line shows: a narrow window follows local features, a wide one shows the shape of the whole sequence.
- Read the figures, then the composition bar, then GC along the sequence. With several records, the table at the bottom compares them and clicking a name switches the detail above.
Worth knowing
- GC and AT are worked out over the bases that are A, C, G or T. Ambiguous bases count towards the length and not towards the percentage, and the screen says how many there were whenever that matters.
- GC skew is (G − C) / (G + C) measured within one strand, from Lobry (1996). It is not a comparison between the two strands: the complementary strand has the mirror-image value by construction, so that reading would be zero everywhere.
- Generated names for headerless records are ASCII on purpose. A FASTA identifier travels into other people's programs, and a non-ASCII one comes back mangled from enough of them.
Questions
Almost always ambiguous bases. If the sequence contains N, dividing by the full length gives a lower number than dividing by the bases that were actually read, and this tool does the second.
It depends what you are looking for rather than on a rule. Wide enough that the line is not noise, narrow enough that the feature you care about is not averaged away.
That G and C appear equally often in the strand you pasted. It is common in sequence that is not under the pressures that produce skew, and it is not an error.
The other sequence tools
- DNA to Protein Translation — Six-frame translation and open reading frames, in any NCBI genetic code.
- Primer Tm Calculator — Melting temperature by the nearest-neighbour model
- FASTA Cleanup — Tidy pasted FASTA and keep the alignment intact.