pssat

An open source tool for aligning two proteins, using secondary structure output predicted by PSIPRED. Developed in Haskell, using wxHaskell for GUI. Produces a visual global or local alignment of two proteins, using the following novel techniques: Uses confidence intervals returned by PSIPRED to determine match scores Affine gap penalty - alignments prefer long, continuous gaps over many short gaps Includes original amino acid sequence for reference Output in HTML format to aid in visualization, or as plain text

example_input.txt
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pssat
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