Review:

"Biocomputing: Informatics and Genome Projects",
Douglas W. Smith
Academic Press

This was an excellent read and quite current, I have highlighted in terse forms some of the topics of personal interest. For more information on the cellular simulation section book I have cross-referenced the Karp work on the Four Rings page.

Topic: Consensus mapping p 96

Tools: BLAST, FASTA

Technique: regular expression searching with metacharacters

Example 1: zinc finger regular expression,

C-X(2,4)-C-X(12)-H-x(3,5)-H which means find amino acid sequences which satisfy:

Cysteine-"two to four amino acids"- Cysteine-", 12 amino acids"-Histadine, _"three to five amino acids" – Histadine

Example 2: G-protein-coupled receptor

[GSTALIVMC]-[GSTAPDE]-{EDPKRH}-x(2)-[LIVMNG]-x(2)-[LIVMFT]-[GSTANC]-[LIVMFYWAS]-[DEN]-R-[FYWCH]-x(2)-[LIVM]

 

Fundamentals of Biomolecular Cryptology p 124

Searching for large collections of functionally equivalent sequences. (FES)

Nucleic Acid classification code:

  1. Regular E1 = {A, C, G, T/U, N} N stands for any of A,C,G, T or U.
  2. E2={R, Y, N} where R stands for purine (A or G) and Y stands for pyrimidine (T or T/U) and N can be R or Y
  3. E3={S,W,N} where S stands for C or G, W standds for A or T/U and N stnads for either S or W
  4. E4={K, M, N}, where K stands for A or C, M stands for G or T, and T can be either K or M.

 

Phylogenetic Analysis and Molecular Evolution p 175

Three categories of tree building methods, parsimony, distance matrix, and maximum likelihood.

Computational Simulations of Biological Systems p 269

ECell: See four rings section under Karp.