The ProteinALIGNment (Palign) programs are a set of programs for sequence searches. They can perform standard dynamic programming, heuristic fasta like searches and profile-profile alignments. Unfortunately the package is not very well documented, but is all available for free under a GPL like license. Palign can be used for many type of alignment problems, it is certainly not always the fastest of all programs but it is very flexible. This webservice can 1. Align two sequences with default values 2) Align two sequences with nonDefault parameters 3) Align two sequences and include their secondary structure information 4) Align a sequence and a structure and get the alignment and a CA-pdb-file 5) Align a sequence and a profile 6) Align two profiles. Amino acid sequence in FASTA format as a string. Amino acid sequence in FASTA format as a string. "Aligns two sequences with default parameters.

Aligns two sequences with user defined parameters. Sequence inputs should be given as strings. Alignment type can be "global", "local" or "gloloc" if not it is set to "global".go,ge and gapmax are integer values.

Aligns two sequences and include secondary structure information (profile files from psiblast).