NW-align: A protein sequence-sequence alignment program by Needleman-Wunsch dynamic programming algorithm Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only Online Services ●I-TASSER ●QUARK ●LOMETS ●COACH ●COFACTOR ●MetaGO ●MUSTER ●CEthreader ●SEGMER ●FG-MD ●ModRefiner ●REMO ●DEMO ●SPRING ●COTH ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●GPCR-I-TASSER ●MAGELLAN ●BindProf ●BindProfX ●SSIPe ●ResQ ●IonCom ●STRUM ●DAMpred ●TM-score ●TM-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14 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) 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. References: Y. Zhang, http://zhanglab.ccmb.med.umich.edu/NW-align yangzhanglabumich.edu | (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218
