"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.
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]
Searching for large collections of functionally equivalent sequences. (FES)
Nucleic Acid classification code:
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.