Extra material for "A study on how to best align protein sequences." Proteins: Struct. Funct. Genet. 46(3):300-309

Programs used in this study.

The LGscore program is avaiilable as source code or as a linux binary. For later (and improved) versions of this program please go here.

The palign program used for the sequence alignments is available here.

Data sets used in this study

The paper contained two set of protein domains-pairs (all sequences are from scop-1.39)

• Set 1 used for training
• Set 2used for testing
• Sequences used here in fasta format
• Scop-1.39 PDB files
• Results for all individual alignments. (unfortunately not very well organized)