Introduction to the Standalone WWW Blast server
This standalone WWW BLAST server suite of programs was designed similar to the regular NCBI BLAST server and such command-line NCBI BLAST programs like "blastall", "blastpgp", "rpsblast" and "megablast". It incorporates most features, which exist in NCBI BLAST programs and should be relatively easy to use. This server does not support any request queuing and load balancing. As soon as the user hits a "Search" button, BLAST starts immediately if entered information is valid. So, this server is not intended to handle large load, which may exist in public service. Such queueing and loadbalancing however may be implemented using such products as Load Sharing Facility - "LSF" from Platform Computing Corporation. Interface to "LSF" was implemented in NCBI, however this was not included in this suite. Standalone server assumes that users have their own BLAST or RPS-BLAST database(s), that should be searched and want to have a simple WWW interface to such search. It is STRONLY recommended that user have experience in installation and running standalone NCBI BLAST programs.
After files are uncompressed, server is ready to be used immediately. Any customizations to the program are welcomed. The source code for WWW BLAST is now part of the NCBI C toolkit, which can be downloaded from the NCBI FTP web site: ftp://ftp.ncbi.nih.gov
The compilation of the NCBI C toolkit includes the WWW BLAST executables. The files in the C toolkit most relevant for the WWW BLAST executables are: wwwblast.c, wwwbutl.c, psiblast.c, wblast2.c.
| February 2, 2004
- All source code moved to the NCBI C toolkit.
- Mouseover feature fixed in graphical overview.
- All binaries synchronized with the latest NCBI C toolkit release. All future
releases will be automatically synchronized with future toolkit releases.
- Recompilation procedure changed. WWW BLAST binaries are now compiled as part
of the C toolkit.
| November 21, 2003
- Fixed a bug with absent images on PSI-BLAST iterations.
- Removed header and progress messages from XML output.
- All binaries recompiled with the newest version of the NCBI C toolkit libra
| May 9, 2003
- Cleaned the Makefile for recompiling the sources.
- Added discontiguous Mega BLAST options.
- Added option to choose a subsequence location for query.
- Added option to choose database genetic code.
- All binaries recompiled.
| April 21, 2003
- Added instructions for recompilation of binaries from the source code to this readme file.
- Fixed a bug in processing of the configuration file that limited allowed number of databases.
- Added images for the Linkout and UniGene links from the BLAST output.
- Corrected paths to the graphical overview for PSI/PHI BLAST output.
- All binaries recompiled with the newest version of the NCBI C toolkit libraries.
| February 10, 2003
- Added support for multi-query XML output.
- All binaries recompiled.
| December 2, 2002
- All binaries recompiled with the newest version of the toolkit.
| August 6, 2002
- Recompiled all binaries to include recent bug fixes.
| June 18, 2002
- Removed limit on the total length of database names.
- Removed xmlblast.cgi and other unneeded XML related files.
- Recompiled all programs.
| January 11, 2002
- Removed formatdb, makemat and copymat binaries from the archive - those should be taken from the NCBI BLAST executables archive
- Added tabular output format
- Added option to mask lower case in query
| May, 2 2001
- No major changes. All programs have been recompiled and made synchronous to the latest NCBI tookit release.
| November 3, 2000
| October, 19 2000
| September, 28 2000
- Added possibility to limit search to results of Entrez query (Regular
| September, 11 2000
- Added MEGABLAST search.
- Added possibility to have multiple FASTA query input - batch searches
with multiple graphical overviews. (Regular BLAST)
| August, 22 2000
- Added new advanced statistics to PSI Blast and ability to produce Smith-Waterman alignments
- Added support for XML output.
| May, 17 2000
- PSI and PHI Blast were added to this distribution
- Added support for client/server interface for gi/accesion
lookups using Entrez
- Added possibility to print Taxonomy reports
- Added option to print alternative alignment with specific color schema
| March, 20 2000
After downloading the file wwwblast.Your_platform.tar.gz to your computer, place it into document directory of HTTPD server and uncompress it by
gzip -d wwwblast.Your_platform.tar.gz
tar -xvpf wwwblast.Your_platform.tar
Please note that parameter "p" in tar options is significant - it will preserve file access options stored in the distribution. Temporary directory for BLAST overview images (TmpGifs) should have 777 permission, and logfiles (wwwblast.log and psiblast.log) should have 666.
After you have uncompressed the distribution file, "blast" directory will be created. You can access sample BLAST HTML input forms using URLs:
This distribution comes with 2 BLAST databases: "test_aa_db" - sample protein database and "test_na_db" - sample nucleotide database. These databases are configured to be searchable immediately with compatible BLAST programs.
Files with suffix "*_cs.*" are analogous to the files without such suffix,
with added capability to make client/server Entrez lookups for sequence
gis and accessions.
- Root directory (./blast):
- BLAST search start-up C-shell files
- Configuration file for the graphical overview image (do not edit!)
- sample BLAST search input HTML forms
- sample MEGABLAST search input HTML forms
- sample RPS BLAST search input HTML forms
- Default configuration file for the WWW BLAST server
- Default configuration file for the PSI/PHI WWW BLAST server
- PSI/PHI BLAST search start-up C-shell files
- sample PSI/PHI BLAST search input HTML forms
- Main PSI/PHI BLAST server executables
- sample BLAST 2 sequences search input HTML forms
- Main BLAST 2 sequences server executables
- CGI used to create 2 sequences alignment image on the fly
- Auxiliary map file for the front BLAST image
- CGI program used to view and delete overview images
- this documentation
- default logfile
- default PSI/PHI Blast logfile
- sample file for full NCBI set of databases
- ./data directory - matrices used in BLAST search
- ./db directory. - Files of test BLAST and RPS-BLAST databases.
- ./docs: - HTML pages used in sample BLAST search input pages
- ./images - images used in the sample BLAST search input pages
- ./Src - source directory for the WWW BLAST server.
- ./Src/XML - source directory for creation of files related to the XML output.
- blstxml.asn - ASN.1 definition for Blast XML
- blstxml.dtd - corresponding DTD
- ./TmpGifs - storage for temporary BLAST overview gif files
To set up databases for the standalone WWW BLAST server, it is necessary to follow these steps:
There is one significant feature of the PSI/PHI Blast server: FASTA
files from which the BLAST databases are formatted should have GI numbers in all
sequence ids. This is almost always true for FASTA files from the NCBI FTP site.
Local databases may not be used with this version of PSI/PHI Blast unless
they have ">gi|12345..." prefix in the definition line.
- Put a file with concatenated FASTA entries in the "./db" directory
- Run "formatdb" program, available from the NCBI ftp site to format the database.
- Add name of the database into server configuration file
- Add name of the database into (PSI/PHI) WWW BLAST search form
Databases for the PSI/PHI Blast should always be created with formatdb using
the "-o T" flag. Test database "test_aa_db" was created using this flag and
database "test_na_db" was created without this flag.
If this distribution is installed not in the "/blast" directory under HTTPD
documents root directory, than path to the distribution should be set
by an environment variable WWW_ROOT_PATH in the file psiblast.cgi or psiblast_cs.cgi
Regular Blast, PSI/PHI Blast, MegaBlast and Blast 2 Sequences have client/server versions for
Entrez gi/accession lookups and printing Taxonomy reports. Configuration of
client/server interface from the user to NCBI should be done the same way as for any
other client/server program to NCBI. If program "blastcl3" works without
problems, this server should work OK as well. If user has firewall - default
configuration will definitely fail to work properly and this case will
require special configuration. If user has problems with such configuration,
one should write to
for further assistance.
Possibility to produce XML output was added to this server. XML definition
of BLAST output is tied to the simple ASN.1 specification designed for this
case. These definitions may be found in the directory ./Src/XML. Any
recommendations on improvements to this (possible) standard may be sent to
XML may be printed by setting "Alignment view" in blast.html or (blast_cs.html)
page to "BLAST XML".
Resulting page will look empty - but if you open the page source (in Netscape -
View -> Page source) - you will see the complete XML document.
Blast 2 sequences program was initially written by Tatiana Tatusova and
Tom Madden and was presented in the article: Tatiana A. Tatusova,
Thomas L. Madden (1999), "Blast 2 sequences - a new tool for
comparing protein and nucleotide sequences",
FEMS Microbiol Lett. 174:247-250.
The standalone WWW version of the program mirrors the NCBI Blast 2 Sequences web page.
RPS Blast or "Reversed Position Specific BLAST" is a
very fast alternative to the program IMPALA. It has the same general
objective - to compare a sequence to a collection of conserved domains (aka motifs, profiles, HMMs).
RPS Blast has a completely different implementation that has
increased the speed of profiles search 10 to 100 times depending on search
conditions in comarison to IMPALA. RPS Blast has an option to perform a translated search of DNA sequences against these conserved domains.
Currently RPS Blast is one of the tools chosen to annotate human
genome at NCBI and is the basis for the CDD Blast search page.
Databases for RPS blast are hardware dependent - for speed reasons. Hence
they are different for big/little endian platforms.
To build RPS database it is necessary to follow the procedure explained in
the file "README.rps", that comes with this distribution.
There is a small RPS database available for testing. This database is a part
of a real NCBI database used in CDD search page. Full NCBI database is
available in platform-independent form from FTP site.
The OOF version of the blastx program finds alignments between a nucleotide
sequence translated into 3 frames and protein sequences, in which query sequence
frames can be shifted within one alignment. The algorithm and low-level alignment
functions were written by Zheng Zhang, currently at Paracel Inc., and incorporated into regular BLAST API by Sergei Shavirin.
XML and tabular output are not yet implemented for the OOF alignments.
This standalone server has a tag convention analogous to the regular NCBI BLAST server. Sample BLAST search forms may be changed to accommodate particular needs of the user in the custom search. Here is the list of these tags and their meaning. If some tag is missing from the search input page, it will take a default value. Exceptions are tags PROGRAM, DATALIB and SEQUENCE (or SEQFILE), that should always be set.
- PROGRAM - name of the BLAST program. Supported values include programs: blastn, blastp, blastx, tblastx and tblastn
- DATALIB - name of the database(s) to search. This implementation includes possibility to use multiple databases. To use multiple databases several "DATALIB" tags should be used on the page for example using checkboxes (look for example at Microbial Genomes Blast Databases BLAST at NCBI). Note, that all of these databases should be properly written in the server configuration file.
- SEQUENCE and SEQFILE - these tags used to pass sequence. First SEQUENCE tag is used for the input sequence. If it is missing, the SEQFILE tag is used instead.
- UNGAPPED_ALIGNMENT - default BLAST search is a gapped search; this tag, if set, will turn gapped alignment off.
- MAT_PARAM used to set 3 parameters at the same time. Value for this tag should be in format " " where mat_name - string name of the matrix (BLOSUM62, etc), d1 - integer for cost to open gap and d2 - cost to extend gap (-G and -E parameters in blastall respectably)
- GAP_OPEN - set value for cost to open gap - 0 or missing tag invoked default behavior
- GAP_EXTEND - set value for cost to extend gap - 0 or missing tag invoked default behavior
- X_DROPOFF - Dropoff (X) for blast extensions in bits (default if zero) (-y parameter in "blastpgp" program)
- GENETIC_CODE - Query Genetic code to use (for blastx only)
- THRESHOLD_2 - Threshold for extending hits in second pass in multipass model search
- MATRIX - Matrix (default is BLOSUM62) (-M in blastall)
- EXPECT - Expectation value (-e in blastall)
- NUM_OF_BITS - Number of bits to trigger gapping (-N in blastpgp)
- NCBI_GI - If formated database use SeqIds in the NCBI format this option will turn printing of gis together with accessions.
- FILTER - Multiple instances of values of this tag are concatenated and passed to the engine as "filter_string" ("L" for low complexity and "m" if filter should be set for lookup table only) - any letter will turn default filtering on - DUST for nucleotides and SEG for proteins (-F in blastall)
- DESCRIPTIONS - Number of one-line descriptions in the output (-v in blastall)
- ALIGNMENTS - Number of alignments to show (-b in blastall)
- COLOR_SCHEMA - Color schema to use in printing of alternative alignment. This option is valid only for blastp and blastn programs. If set - it will
override option set by "ALIGNMENT_VIEW"
- TAX_BLAST - Print taxonomy reports. This option is valid only for
client/server version of regular Blast
- XML_OUTPUT - Print XML Blast output. All other alignment view options will be disabled
- ENTREZ_QUERY - Limit search to results of Entrez query. Only for
- RPSBLAST - This tag with turn "blastp" or "blastx" search into RPS Blast search for the rps blast database.
- OOF_ALIGN -This flag if set to non-zero digit will turn on OOF alignment for "blastx" and will set frame shift penalty to this value.
- OTHER_ADVANCED - this tag allows to input string analogous to the command line parameters of blastall. Setting parameter in OTHER_ADVANCED tag will override all other settings of this parameter. Supported options include:
- -G gap open cost
- -E gap extend cost
- -q penalty for nucleotide mismatch
- -r reward for nucleotide match
- -e expect value
- -W wordsize
- -v Number of descriptions to print
- -b Number of alignments to show
- -K Number of best hits from a region to keep
- -Y effective search space
- ALIGNMENT_VIEW - will set type of alignment to show. Available options include:
- 0 - Pairwise
- 1 - query-anchored with identities
- 2 - query-anchored without identities
- 3 - flat query-anchored with identities
- 4 - flat query-anchored without identities
- 7 - BLAST XML (equivalent to setting the XML_OUTPUT tag)
- 9 - Hit Table - to produce tabular output
- OVERVIEW - used to turn on or off printing of alignment overview image
- BLAST_TYPE - a special tag to distinguish different BLAST search types. See the description of a configuration file.
Default configuration file is "blast.rc" and logfile "wwwblast.log". Setting tag BLAST_TYPE to specific value may change these names. This is useful if few different search input pages use the same CGI search engine, but significantly different by content and priorities. A sample configuration file comes with this distribution:
This file will set how many CPUs will be used in the BLAST search and what databases may be used with what programs. Logfile currently stores only limited information but also may be updated by programmers to store more values in it. Please note, that usually HTTPD servers run by accounts that do not have write access to disk, so the logfile permission should be set to 666.
There is a way to debug these programs.
This should do your problematic search without WWW. If this resulted
in coredump - you may look into the core file with:
- Add line "setenv DEBUG_COMMAND_LINE TRUE" into the *.cgi file
- Run search that results in the problem - this should create a
file "/tmp/__web.in" in the "/tmp" directory.
- Set all necessary environment variables on the command line (BLASTDB at least)
and run from command-line: "blast.REAL < /tmp/__web.in"
dbx blast.REAL core
and then use command "where" to print stack.
BLAST Help Desk
Last modified: Fri Jan 11, 2002