| NCBI BLAST FTP Site | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Tao Tao, Ph.D. User Service NCBI, NLM, NIH | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TOC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 1. Introduction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| NCBI BLAST ftp site (ftp.ncbi.nlm.nih.gov) provides software packages for standalone blast, client server blast, and wwwblast packages for various platforms. It also provides commonly used blast databases in preformatted as well as FASTA format. Documents on the blast executables and other related subjects are also available from this site. This file describes the the subdirectories and files found on this ftp site. It also prvoides the basic information on file content and on how the files should be used. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2. File list and content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This section list and describes the files found on the BLAST FTP site. File content for each directory/subdirectory is described in a separate table. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.1 ftp.ncbi.nlm.nih.gov/blast/ general directory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The blast ftp directory contains several subdirectories each for a specific set of files. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.2 /blast/db/ directory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Databases larger than two gigabytes (2 GB) are formatted in multiple 
volumes, which are named using the "database.##.tar.gz" convention. 
All relevant volumes are required. An alias file is provided so that 
the database can be called using the alias name without the extension 
(.nal or .pal). For example, to call est database, simply use "–d est" 
option in the commandline (without the quotes). 
Certain databases are subsets of a larger parental database. For those 
databases, mask files, rather than actual databases, are provided. The
mask file needs the parent database to function properly. The parent 
databases should be generated on the same day as the mask file. For 
example, to use swissprot preformatted database, swissprot.tar.gz, one 
will need to get the nr.tar.gz with the same date stamp.
To use the preformatted blast database file, first inflate the file 
using gzip (unix, linux), WinZip (window), or StuffIt Expander (Mac), 
then extract the component files out from the resulting tar file using 
tar (unix, linux), WinZip (Window), or StuffIt Expander (Mac). The 
resulting files are ready for BLAST. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.2.1 /blast/db/FASTA/ subdirectory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The FASTA database files are now stored in this subdirectory, it does 
contain some additional databases that are not available via the NCBI 
BLAST pages. Due to file size issues, the full est database is not 
provided. One needs to get the three subsets and concatenate them 
together to get the complete est database.
These databases will need to be formatted using formatdb program found 
in the standalone blast executable package.  The recommended 
commandlines to use are: formatdb –i input_db –p F –o T for nucleotideFor additional information on formatdb, please see the formatdb.html at: /blast/documents/formatdb.html 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.3 File content for /blast/demo/ directory | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains some technical presentations from the BLAST 
developers along with some demo tools or documentation relevant to BLAST. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.4 File content for /blast/documents/ directory | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains copies of the documentation on different BLAST 
programs distributed from this ftp site under the /blast/executables/ 
directory. blast.txt also contains detailed release history. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.5 File content for /blast/executables/ directory | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains several subdirectories each for a specific subsets of executable BLAST programs. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.5.1 File content for /blast/executables/LATEST/ subdirectory | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains the latest official release of precompiled BLAST executable programs.
The binaries can be divided into three groups. blast initialed files are equivalent. They contain
the standalone command line blast binary programs for different platforms. Users need this package
to set up BLAST locally. It also provides the tools necessary to prepare custom databases 
and retrieve sequences from these prepared databases.  
The netblast initialed archives the blastcl3 program which functions by 
formulating BLAST search locally first before forwarding the search to NCBI 
blast server for process. The search results returned by NCBI BLAST server 
is saved to an user-specified file on local computer disk. Users do not need to maintain local databases, nor can
they search custom databases locally.
 
The wwwblast initialed archive contains the web pages with embedded blast search 
forms similar to that of NCBI. They can process the BLAST request submitted through web and search against 
local set of databases and return the result to a browser window. wwwblast 
is now in sync with the NCBI toolkit and the two above two packages. Installation requires existing web server (apache) setup. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.5.2 /blast/executables/release/ subdirectory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains past major releases of BLAST, as far back as version 2.0.10. Each release is in its own subdirectory. 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.5.3 /blast/executables/snapshot/ subdirectory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains compilation of blast packages with bug fixes in between major versioned releases. The subdirectories are named with date. There was not snapshot or patch since the end of 2004, which as for release 2.2.10. Available old patches will not be listed here. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.6 /blast/matrices directory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| This directory contains the scoring matrices, which are files that can be used by BLAST alignment assessment. The file are text files with special format that can be viewed directly by a browser. For valid statistical analysis, blastn uses only identity matrix and blastp only supports a limited subset of the BLOSUM and PAM matrices: BLOSUM45, BLOSUM62, BLOSUM80, plus PAM30 and PAM70. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2.7 /blast/temp/ directory content | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| For temporary file storage and miscellaneous files or tools. Current empty. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3. Techinical Support | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Additional questions/comments on this ftp site should be directed to 
NCBI blast-help group at: blast-help@ncbi.nlm.nih.govOther questions on general NCBI resources should be directed to: info@ncbi.nlm.nih.gov | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||