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User Service, NCBI, NLM ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/The archive for Window PC is provided as a self extracting archive. It is named in the following convention: blast-#.#.#-ia32-win32.exeFor PC with 64 bit chip and running Windows 2003 or better, use the following binary instead: blast-#.#.#-x64-win64.exeHere the string #.#.# represents the current version number. If a patched version is made in between official releases, the #.#.# will be the date of the patch. To download using a browser, type "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/" without the quote to log on to NCBI BLAST ftp site. Right clicking on the correct archive and select "Save link as ..." from the popup menu. Follow the prompt to select the desired location to save the archive. 2. Installation To facilitate the file management by keeping all the relevant files/directories from the archive in one central location, we need to create a new subdirectory under E:\ directory [1], named as blast-#.#.#, with #.#.# indicating the version number. For version 2.2.15, we will name this subdirectory blast-2.2.15. Move the donwloaded blast archive to this subdirectory and double click to extract the content. We should see a DOS terminal window open briefly with file names flashing by. This installs the blast package and creates three subdirectories under blast-2.2.15: bin, data, and doc. The bin subdiretories contains the following programs: bl2seq.exe blastall.exe blastclust.exe blastpgp.exe copymat.exe fastacmd.exe formatdb.exe formatrpsdb.exe impala.exe makemat.exe megablast.exe rpsblast.exe seedtop.exeThe documents on individual programs are under the doc subdirectory. The data subdirectory contains score matrices needed for scoring protein alignments. Additional files needed by other NCBI programs, such as sequin and Cn3D, are also included. For better management of database files, we also need to create a subidrectory named db under blast-2.2.15 [2].
[1] E:\ is only suggested destination, used as an example. [NCBI] DATA=E:\blast-2.2.15\data [BLAST] BLASTDB=E:\blast-2.2.15\dbSteps needed to created this file on PC are the following:
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| Figure 3. Configure standalone BLAST using WINDOWS environment variable. Top-left is initial system popup. Top-right is the Advanced tab of system popup. Clicking on "Environment variable" button will bring out lower-left popup. You can see the variables already specified: BLASTDB (e:\blast-2.2.15\db) and PATH (e:\blast-2.2.15\bin). The later adds e:\blast-2.2.15\bin to the executable search path, so we can call BLAST programs from any directories. Clicking on "new" button (B) will bring out new popup in lower-right. The example in lower-right (C) specifies the DATA directory and points it to "e:\blast-2.2.15\data". |
One may still need the ncbi.ini file if netblast is also installed since it stores the firewall configuration settings needed
by
blastcl3. See netblast.html for more information.
4. Execution
To run the program, we need first launch a DOS command prompt by clicking on
"Start ⇨ Program ⇨ Accessories ⇨ Command Prompt" as shown in the screenshot (Figure 4.1).
In the DOS prompt window, change the working directory to "E:\blast-2.2.15" by typing "E:" and enter key stroke, followed by "cd blast-2.2.15" and enter key stroke. To create the db directory, use "mkdir db" command. Sample commad lines are listed in Table 4.1 for your reference.
To make windows aware of the location of blast programs, we need to add the path "E:\blast-2.2.15\bin" to the PATH environment variable. See Figure 3. After this, we will be able to call the programs using their name from any directory in the computer. For example, to do the following tasks: We will use this command line: blastall -p blastn -d refseq_rna -i fasta_query.txt -o ouput.txt To further customize the search, we can manipulate the relevant search parameters. For more details, see the Section 3 of Program Parameters for blastall. Note, refseq_rna is a NCBI provided database, available from the db subdirectory (ftp.ncbi.nih.gov/blast/db) in preformatted form. For more information, please see: blastdb.html. For questions, feedbacks, and technical assistance, please contact blast-help at: blast-help@ncbi.nlm.nih.govFor questions on other NCBI resources, please write to: info@ncbi.nlm.nih.gov | ||||||||||||||||||