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
