Biology Reference
In-Depth Information
Fig. 5 The user interface of PRALINE server
submitted is 500 with a maximum length of 2,000 residues for each
sequence. This is to limit the server load and is not due to any
limitation of the PRALINE algorithm itself.
On the main page (Fig.
5
), the user can manually set the gap
opening and gap extension penalties, choose the appropriate sub-
stitution matrix, and set the parameters for various alignment stra-
tegies available in PRALINE. The default setting is 12 for gap open
penalty, 1 for gap extension penalty, and BLOSUM62 as the amino
acid substitution matrix. Other amino acid substitution matrices
