The NCBI BLAST executable, version 2.2.27+ (Camacho et al., 2009), was used to match the protein products from the CHO genomes, the contigs from the CHO transcriptome, the proteins from the CHO proteome, mouse secretome, the human genome, and the validated CHOP sequences.
The whole-genome BLAST distances between two genomes were calculated with alignments inferred with the bl2seq program of the NCBI BLAST executables (version 2.2.18) with default parameters.
The Embed3GL program executables for 32/64-bit 32/64-bitlong Windowse user's malong and usage examples are freely available at the withpage [ 20].
This procedure used Perl scripts, Perl DBI, and Bioperl (Stajich et al. 2002), where sequences were retrieved from the MySQL database and compared using the BLAST executables (version 2.2.23) with protein databases created using the formatdb tool.
TBLASTN searches were carried out in this local database applying the BLAST+ 2.2.26 executable application available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ with the known human SSTR sequences as well as the identified coelacanth sequences as search queries.
The Mac Kermit m680x0 executable in BinHex 4.0 format.
To view the layout of a particular executable, run objdump (80x86) or i386-elf-objdump (SPARC) with the -p option.
A BLAST+ v.2.2.24 executable was downloaded from the NCBI FTP site (ftp://ftp.ncbi.nih.gov/blast/executables/blast+/).nih.gov/blast/executables/blast+/
As shown in the figure, the executables of the SPEC2000 benchmark programs are processed in the simulator to collect the following data for the tested caches: prediction hit rate, power consumption amount, cache miss rate, and latency.
Design of cyber-physical systems today relies on executable models.
If the original method had been published in executable form and preserved until today, such discrepancies could have been avoided.
