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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)

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• Click NWalign to download the executable program for Linux system. Simply running the program itself will give you a brief instruction of how to use it (In case that you are using a 32 bit computer and you get warning message of "bash: ./NWalign: cannot execute binary file", you need to download the source code and compile the program on your machine. See below).
• Click NWalign.f to download the source code of NW-align coded in Fortran77. You can compile the program in your computer by
  >gfortran -static -O3 -ffast-math -lm -o NWalign NWalign.f
  or
  >g77 -static -O3 -lm -o NWalign NWalign.f
• Click NWalign.java.tar.bz2 to download a Java version of the NW-align code.
• Click SWalign.java.tar.gz to download a Java version of the SW-align code, which was designed to align two protein sequences using the standard Smith-Waterman algorithm. Different from NW-align which is for global sequence alignment, SW algorithm is designed for optimal local sequence alignments.
• click BLOSUM62.txt to download the BLOSUM62 Substitution Matrix that is used in the NW-align program.

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