I have implemented in C an API for reading data from NCBI
1. Much easier to use than the NCBI toolbox.
2. On my linux box the demo program is about 33% faster than
fastacmd at dumping a database into a fasta formatted text file.
3. Correctly decodes the binary ASN.1 headers for all of
the BLAST databases on my system.
4. Retrieve by gi number or entry order (1->N).
5. Retrieve ACGT or degenerate form of DNA sequences.
6. Free for use in free software. Contact me or Caltech if
a license for commercial purposes is required.
Not yet tested on any 64 bit platform. Probably the header
file will need to be tweaked slightly in order to run there.
Please report bugs.
mathog at caltech.edu