davidhyongae2 / pairwise_sequence

protein sequence correlation between position i and j

pairwise_sequence calculator

Running sequence comparision at position i and j based on physiochemical score:

1. Structure of proteins: packing of alpha-helices and pleated sheets.
   PNAS (1977), Vol. 74, No 10. p. 4130-4134.
   
2. Based on the review by Cyrus Chothia pioneer of structural bioinformatics
   Average Volume per residue taken from Ann. Rev. Biochem. (1984) 53, 537-72.
   
3. Conformation of amino acid side-chains in proteins.
   JMB (1978) 124, 357-386.
   
4. Code is based on this great paper: Nucleic acids res.(2004) W64-W67 doi: 10.1093/nar/gkh451.
   CRASP: a program for analysis ofcoordinated substitutions in multiple alignments of protein sequence.

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(Step1) align_pairwise('seq1','ChotVol.txt',0.8,0,-0.8,0)
[matlab will automatically generate a heatmap]

(Step2) run heatmap_raindbow.r to generate Heatmap using ggplot2