PEPINFO
PEPINFO. Detects and displays various useful metrics about a protein sequence; plots simple amino acid properties in parallel. It can display and plot the following properties: hydrophobicity (using the method of Kyte & Doolittle, 1982); of optimal matching hydrophobicities (OMH; Sweet & Eisenberg, 1983), or of consensus parameters (Eisenberg et al., 1982); and a histogram of the presence of residues with the physico-chemical properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Positive, Negative.
PEPINFO Algorithms
- Kyte J, Doolittle RF (1982) "A simple method for displaying the hydropathic character of a protein" J Mol Biol 157(1):105-132.
- Sweet RM, Eisenberg D (1983) Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 171(4):479-488.
- Eisenberg D, Weiss RM, Terwilliger TC. (1982) "The helical hydrophobic moment: a measure of the amphiphilicity of a helix" Nature 299(5881):371-4.
If you use EMBOSS, please cite: Rice, P, Longden, I, and Bleasby, A (2000) " EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics 16, (6) 276--277. Original program "HELIXTURNHELIX" (EGCG 1990) by Peter Rice (pmr © ebi.ac.uk)
Manual: pepinfo.html
INPUT = Protein Sequences.
TEST INPUT FILES
Input file: pepinfo_in.txt
TEST OUTPUT FILES
Output file: pepinfo_out.1.png
Output file: pepinfo_out.2.png