ReadFasta version 0.35a

Toshinori Endo tendo at fas.harvard.edu
Tue Dec 29 23:17:17 EST 1998


Now I updated the C++ class library for FASTA data format sequence,
ReadFasta version 0.35
at http://toshi-pc.fas.harvard.edu/pub/ReadFasta/ReadFasta-0.35a.tgz

Thank you for those who downloaded ReadFasta library and
I would like to ask you for downloading the latest one.
I made several improvement from the last version.
The major points are:

    1. The Sequence class is now the inherited class of string.
        This means you can use any functionality of string class on
        Sequence class.  Previous seq() method is still available.

    2. CodonTable class  for translation codon table is added.
        The number of codon tables are corresponding to the
        qualifier values of DDBJ/EMBL/GenBank databases.

    3. Several bugs are fixed and codes are improved.

    4. All the site number is changed to start from number 0
        instead of 1.

    5. README file (containing manual) is updated.


Here is a short description of ReadFasta.

    1. C++ class library for FASTA data format sequence file
        which allow semicolon (;) as the secondary comment
        character.

    2. To read FASTA data format file is just 

            Sequence seq;
            cin >> seq;

        Identifiers, comments and sequences are recognized by
        class and they are classified accordingly.
        To access those data, just use the methods id(), rem()
        and seq().  For individual site, you can use operator[].
        For fragment, you can use seq(start,end).

    3. Multiple sequence and Clustal format alignment are also
        accessible by MultiSeq and AlignedSeq class in the library.
        
    4. Codon table is provided now for DNA sequence.



I plan to expand the library for 

    1. GenBank format sequences
    2. Dynamic programming algorithms
    3. Genetic distance programs
    4. Phylogenetic trees.
    5. Windows and Macintosh versions


Comments and suggestions are welcome.


Toshinori Endo
Harvard University Biological Laboratories
tendo at fas.harvard.edu







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