ALIGN
ALIGN produces an optimal global alignment between two protein or DNA sequences. ALIGN will automatically decide whether the query sequence is DNA or protein by reading the query sequence as protein and determining whether the `amino-acid composition' is more than 85% A+C+G+T. Align uses a modification of the algorithm described by E. Myers and W. Miller in "Optimal Alignments in Linear Space" CABIOS (1988) 4:11-17. The program can be invoked either with command line arguments or in interactive mode. align weights end gaps, so that an alignment of the form -----MACF SRTKIMACF will have a higher score than: MACF MACF. ALIGN0 uses the same algorithm, but does not weight end gaps. Sometimes this can have surprising effects. Part of FASTA.
If you use this tool, please cite: Pearson WR, Lipman DJ (1988) "Improved tools for biological sequence comparison." PNAS USA 85(8):2444-8.
Manual: http://www.med.nyu.edu/rcr/rcr/fastaman.html
Related Programs: LALIGN - Local nucleic acid and protein sequence alignment; PLALIGN - Plots of local nucleic acid and protein sequence alignment
INPUT = Nucleic Acid and Protein sequence files in fasta format.
TEST INPUT FILES
Input file: alignn1_in.txt
Input file: alignn2_in.txt
TEST OUTPUT FILES
Output file: align_nuc_out1.txt