Announcement: molbio++, a C++ library for biosequence analysis

"robison1 at husc10.harvard.edu" at HUSC3.HARVARD.EDU "robison1 at husc10.harvard.edu" at HUSC3.HARVARD.EDU
Wed May 5 10:21:00 EST 1993


molbio++, release 0.01, is now available via anonymous ftp from:

			golgi.harvard.edu
			pub/CONTRIBUTIONS/molbio++


molbio++ is a C++ library for molecular biosequence analysis.  Major features
include:


	classes and services for
	     reading and writing sequence data in the following formats:

			Genbank Flatfile
			EMBL / SwissProt
			GCG / Wisconsin
			Fasta / Pearson
			PIR
			NCBI Retrieve Server (read-only)

	     limited parsing of fields and features in biosequence files

	     storing amino acid or nucleic acid sequences

	     iterating over a biosequence

	     calculating and storing counts or frequencies of amino acids
		or nucleotides

	     device-independent graphics, via GCG's FIGURE program

	     translating nucleotide sequences into proteins using
	       the universal genetic code or modifications thereof.

	     parsing BLAST output

	     calculating pI and molecular weight of proteins

	     amino acid hydropathy values of Kyte & Doolittle

	
	example programs for

		reformatting biosequence files
		
		extracting open reading frames from nucleotide sequences

		parsing BLAST output

		calculating isoelectric point and molecular weight of proteins

		codon usage plots

		calculating local %GC for nucleotide sequences

		finding restriction sites in nucleotide sequences


	
The examples in molbio++ are not meant to replace existing programs
(they are almost universally superior in functionality), but rather to
demonstrate the classes and provide bases for customization.


molbio++ is the result of an ongoing individual research project.  I 
apologize in advance for any trouble it may give you, but cannot be
held liable.  

At this point, molbio++ has only been tested with cfront running on
a Sparcstation.  In general, there should be very few compatibility 
problems.  UNIX-specific features are confined to a single class,
and no templates are used.  

The mention of any commercial products in molbio++ and its accompanying
documentation does not constitute an endorsement, but simply reflects what
I have available for use.


If you attempt to use the libraries, please send a message to:

		robison at biosun.harvard.edu

(N.B. it's robISon, not robINSon; someone else gets it there)



Announcements of general updates to molbio++ will be posted to 

		bionet.software


Major announcements (major revisions, change in ftp site, etc)
will also be posted to comp.lang.c++ and bionet.announce.


An earlier version of the library was distributed under the name
"kertools".  molbio++ is completely incompatible with kertools,
as the result of a major rewrite.  If you have software written
for kertools, I can lend some advice as to how to convert.



Acknowledgements:

	KR is supported by a National Defense Science Fellowship,
and uses computers funded by the Department of Energy, the National 
Institutes of Health, and the Howard Hughes Medical Institute.  Development
of the library has been driven by challenges given me by Dr. Walter Gilbert
and Dr. George Church.  I have benefitted from discussions with Gary Gryan
and Peter Jensen.  Finally, I would have never gotten around to learning
C++ if it were not for the gift of Stroustrup from my brother, Arch Robison.


Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics (Harvard Medical School) / HHMI
robison at biosun.harvard.edu



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