DNA sequence analyzer
A ↔ T
Paste a DNA sequence (FASTA, raw, with or without position numbering): the tool normalizes it, flags invalid characters, computes base composition and GC content, and produces the complement and reverse complement. IUPAC ambiguity codes are handled explicitly, without ever inventing a precision the sequence doesn't support.
Scientific dossier
What the tool computes, what it assumes, where it stops being valid, and where its data comes from.
Method & formulasA ↔ T
A ↔ T
G ↔ C
In double-stranded DNA, each base pairs with its complementary base following the Watson-Crick rule: adenine (A) with thymine (T), guanine (G) with cytosine (C). This rule extends to ambiguous IUPAC codes (e.g. R, purine A/G, complements to Y, pyrimidine C/T).
- R
- · purine, A or G.
- Y
- · pyrimidine, C or T.
- S
- · strong, 3 hydrogen bonds, G or C.
- W
- · weak, 2 hydrogen bonds, A or T.
- K
- · keto, G or T.
- M
- · amino, A or C.
- B, D, H, V
- · any base except A, C, G or T respectively.
- N
- · any base, A, C, G or T.
Validity domainAn exact GC content is only shown when every position in the sequence has a certain GC status.
An exact GC content is only shown when every position in the sequence has a certain GC status. As soon as an ambiguous code could correspond to a GC base or not (for example R, N). The tool shows a range rather than inventing a single value. Except for S and W, whose two possible bases share the same GC status (always for S, never for W), in which case the rate stays exact despite the exact base being ambiguous. GC content alone is not enough to conclude on a sequence's stability or its actual melting temperature: those also depend on length, base order (stacking) and experimental conditions (ionic strength, concentration).
GC content: definitionGC content is the proportion of guanine (G) and cytosine (C) bases in a sequence, expressed as a percentage.
GC content is the proportion of guanine (G) and cytosine (C) bases in a sequence, expressed as a percentage. It varies widely between organisms and genome regions, and influences physical properties of DNA (G-C pairs, with 3 hydrogen bonds, are more thermally stable than A-T pairs, with 2).
Complement and reverse complementThe complement replaces each base with its complementary base, in the same reading order.
The complement replaces each base with its complementary base, in the same reading order. The reverse complement performs the same substitution and then reads the result backwards: this is what corresponds to the strand actually paired in double-stranded DNA (the complementary strand reads in the 5'→3' direction opposite the reference strand), and it's this sequence that's used to design a primer on the opposite strand.
Worked exampleGAATTC is the restriction site recognized by the EcoRI enzyme: it is a biological palindrome, its reverse complement is identical to the original sequence, a property characteristic of double-stranded restriction sites.
GAATTC is the restriction site recognized by the EcoRI enzyme: it is a biological palindrome, its reverse complement is identical to the original sequence, a property characteristic of double-stranded restriction sites.