This is the README for a test suite of the BLAST programs.

The test suite includes:

1.) this README.

2.) test.csh, a c-shell script demonstrating how to run the
BLAST jobs.

3.) four protein query files.  Each protein query file starts
with 'aa', e.g. aa.p38398.

4.) six nucleotide query files.  Each nucleotide query file
starts with 'nt', e.g., nt.3283410.

To run the test suite one needs:

1.) executables for blastall and megablast.  One may obtain
precompiled binaries for many platforms from ftp://ncbi.nlm.nih.gov/blast/executables/  
The NCBI toolkit source code (including BLAST) may be obtained from 
ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/  To compile this follow the
instructions in the appropriate readme file (e.g., readme.unx or readme.dos)
which can be found in the 'ncbi/make' directory after dearchiving.  Please send 
questions about compiling the NCBI toolkit to 'toolbox@ncbi.nlm.nih.gov'.

2.) BLAST databases for nt, nr, and htgs.  Preformatted BLAST databases
for these three may be obtained from ftp://ncbi.nlm.nih.gov/blast/db/FormatedDatabases/
Otherwise one may use FASTA files (e.g., text) from ftp://ncbi.nlm.nih.gov/blast/db
and the BLAST database formatter formatdb (which is included with the executables
and can also be compiled from the source code) to turn the FASTA into BLAST databases.  
The BLAST databases contain the nucleotide sequences in compressed format and are 
smaller than the corresponding FASTA files.  Unless one wishes to perform test runs 
against other databases than those from the NCBI it's easier to take the preformatted ones.

Note on performance tests: BLAST is meant to run on a machine with the
entire BLAST database memory-mapped; if it is necessary to read the
database from disk during the search it will be very slow.   A test machine
should have enough memory to keep the database in memory and one or more
runs against a database should be performed (to ensure that it is in memory)
before profiling the search.

This test suite is still under development and may include significant
additions in the near future.

One should also look at README.bls and README.mbl in ftp://ncbi.nlm.nih.gov/blast/documents/
The former describes how to setup and run BLAST, the latter concerns megablast.
