A C++ class for sequences ?

Pierre Lindenbaum lindenb at biotec.jouy.inra.fr
Tue Oct 19 03:34:36 EST 1999


	Thank you !

	I found it at 

	ftp://ftp.ebi.ac.uk/pub/software/unix/molbio.tar.Z


		Pierre LINDENBAUM




> Keith Robison made such a version available at one time called molbio++,
> but the 1st few google hits were 404.  I have a copy somewhere if you can't
> find it on an archive.
> 
> 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 
> 
>    ftp from golgi.harvard.edu (128.103.161.55) 
>    in pub/CONTRIBUTIONS/molbio++ 
> 
> 
> From personal experience, I'd rec Jim Knight's seqio pkg (C not C++, but
> you could wrap it) for sequence handling and manipulation.  Also
> net-available, altho gone from it's old primary UC Davis home.  Again, I
> can send it to you if can't find it.
> 
> Best
> harry
> 
> 
> 
> 
> 
> 
> 
> Pierre Lindenbaum wrote:
> > 
> >         I'm a looking for a C++ class handling biological sequences...
> > 
> >         Is there a "standard" class ? Does it exist ? where ?
> > 
> >         Thank you in advance.
> > 
> >                 Pierre LINDENBAUM
> 
> 






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