LALIGN is a program that compare two sequences looking for 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 search reports only the best alignment between the query sequence and the library sequence, LALIGN will report a specified number of alignments (the default is 10) between the two sequences and also shows the actual local alignments between the two sequences and their scores.
The LALIGN/plalign/fasta programs use a standard text format sequence file. Lines beginning with '>' or ';' are considered comments and ignored; sequences can be upper or lower case, blanks,tabs and unrecognizable characters are ignored. LALIGN/plalign expect sequences to use the single letter amino acid codes.