Wanted: C++ Libraries for Biological Sequences

Keith Robison robison1 at husc10.harvard.edu
Mon Jan 11 10:28:50 EST 1993


My own set of C++ libraries is undergoing a rewrite to improve
their design and reliability.  I will post a message to this
newsgroup when that rewrite is done identifying an ftp source.

These libraries provide basic functions for manipulating and 
analyzing nucleic acid and DNA sequences, as well as simple
GenBank parsing capabilities and an interface to the
device-independent graphics package contained within
the GCG sequence analysis package.  Also included are
a set of sample programs which demonstrate using the libraries
to:

	translate DNA/RNA into protein
	extract all open reading frames from a DNA/RNA sequence
	perform simple parsing of GenBank flat-files
	perform simple parsing of BLAST output
	look for oligonucleotide repeat regions in DNA
	look for protein regions likely to form coiled-coils
	generate GCG-compatible codon usage tables from sets of sequences
	search for restriction sites in DNA




Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison at biosun.harvard.edu 




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