DNA sequence analyzer

Base composition, GC content, complement and reverse complement of a DNA sequence pasted as FASTA or raw text, with or without numbering. Invalid characters are flagged; IUPAC ambiguity codes are handled.

In double-stranded DNA, adenine (A) pairs with thymine (T) and guanine (G) with cytosine (C) (Watson-Crick rule). Ambiguous IUPAC codes follow the same rule: the complement of R (A or G) is Y (C or 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.

An ambiguous code that may stand for either G/C or A/T (R, N…) gives a GC content as a range; S (G or C) and W (A or T) keep it exact. A sequence’s stability and melting temperature also depend on length, base order (stacking), ionic strength and concentration.

GC content is the proportion of guanine (G) and cytosine (C) in the sequence, as a percentage. It varies between organisms and genome regions. G-C pairs, with 3 hydrogen bonds, are more thermally stable than A-T pairs, with 2.

The complement replaces each base with its complementary base. The reverse complement reads it backwards: it is the paired strand, read in its own 5'→3' direction (the strands are antiparallel), used to design a primer on the opposite strand.

GAATTC is the recognition site of the restriction enzyme EcoRI. It is a palindrome: its reverse complement is the sequence itself, as for most sites of type II restriction enzymes.