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NW-align is simple and robust alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penalty=-11 and gap extension penalty=-1. The source code of this program can be downloaded at the bottom of this page, which can be easily modified for different purposes. A Java code using the standard Smith-Waterman algorithm for local sequence alignment was recently added in the page as well.

Please copy and paste your first sequence here (<6,000 residues, in FASTA format):

Or upload the first sequence from your computer (in either FASTA or PDB format):

Please copy and paste your second sequence here (<3,000 residues, in FASTA format):

Or upload the second sequence from your computer (in either FASTA or PDB format):

Email: (optional, where results will be sent to)

ID: (optional, your given name of the proteins)






References:
Y. Zhang, http://zhanglab.ccmb.med.umich.edu/NW-align

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