LALIGN
LALIGN: compares two protein/DNA sequences for local similarity and shows the local sequence. LALIGN and PALIGN programs compare two sequences to identify local sequence similarities. LALIGN uses code developed by X. Huang and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the "SIM" program. While SSEARCH reports only the best alignment between the query sequence and the library sequence, LALIGN will report a specified number of alignments (default = 10) between the two sequences. LALIGN shows the actual local alignments between the two sequences and their scores. Part of the FastA family.
Manual: http://www.med.nyu.edu/rcr/rcr/fastaman.html
INPUT = A Nucleic Acid or Protein sequence file in fasta format. The search set is a single target sequence.
TEST INPUT FILES
Input file: lalign1_in.txt
Input file: lalign2_in.txt
TEST OUTPUT FILES
Output file: lalign_out1.txt