OOP and molecular biology

[Keith Robison]

Two addenda on the C++ in biology posting:

1) An extensive system of C++ programs for manipulating E.coli genetic
   data is described in:

	DG Shin, C Lee, J Zhang, KE Rudd, and CM Berg.  1992.  CABIOS 8:227-238
	Redesigning, implementing, and integrating Escherichia coli genome
	software tools with an object-oriented database.

2) My rudimentary C++ library is available from golgi.harvard.edu
   in directory ftp/pub/contrib/kertools.  Within are a number
   of libraries for general sequence and GenBank flat-file
   handling.  Programs in the directory include ones for:

	Manipulating data in GenBank flatfile format.
	Translating DNA to protein, including extraction of ORFs
	 to separate sequences and generation of codon usage tables.
	Detecting coiled-coil regions in proteins by the method
  	 of Lupas et al (Science 252:1162-1164).
	Condensing output from NCBI's BLAST
	Detecting repetitive DNA sequence regions by the method of
	 Tautz et al (Nature 322:652-656) [soon - coded but not tested].

These tools and the underlying class library are still in a very fluid
state, but if you send me an E-mail note I will keep you informed as
to updates and changes.  All feedback will be appreciated.


Keith Robison
Harvard University
Program in Biochemistry, Molecular, Cellular, and Developmental Biology

robison at ribo.harvard.edu