AUG_hairpin: program for prediction of a downstream hairpin potentially increasing initiation of translation at start AUG codon in a suboptimal context.

It has been experimentally shown that a downstream hairpin in certain positions with respect to start codon could compensate in part for the suboptimal AUG context (Kozak, 1990; see Tutorial for details). Basing on this observation, AUG_hairpin program predicts the stem-loop structures whose 5-borders are located within the critical region (from 11th to 18th nucleotides by default; the borders can be adjusted)

Tutorial

Enter nucleotide sequence of 5'-untranslated region (preferably 10 nucleotides upstream the start AUG codon; do not include AUG). Notes: (plain sequence or FASTA-format may be used; no gaps are allowed; only a,t,g,c symbols may be used).


Enter the 5-end segment of a nucleotide sequence of a protein coding region (~100 nucleotides starting from the start AUG codon)

Min position for hairpin start:

Max position for hairpin start (<= 30):

Detect only perfect helices:

Max bulge or interior loop size if imperfect helices are allowed:

Example