YAP: Yet Another Alignment Program*
Pairwise Sequence Alignment Using Secondary Structures

(*)Download it here

First Sequence Name (optional)

Paste Your FIRST sequence

Paste Your FIRST "Secondary Structure" (see allowed alphabet)

Second Sequence Name (optional)

Paste Your SECOND Sequence

Paste Your SECOND "Secondary Structure" (see allowed alphabet)

Select Score Matrix: 
Score the ending gap penalties 

Open gap penalty

Open extension penalty

Weight score (secondary structure only = 0.0 / sequence only = 1.0) 1.0<= w <=0.0)

Amplification factor for gap opening in the secondary structure segments (>=1.0)

Upload secondary structure score matrix a file (leave ti blank if you want to use the internal) :


Press   to align (and please wait)