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DroSpeGe Blast ServiceFeature type keyRefering to the key below, any assembled chromosomes or ultrascaffolds will show up as C or S types, and be searched with the "Chromosomes or Scaffolds" feature type.If there is a predicted gene set for the genome, they show up in the G section, and likewise for translations of these showing up in the P section. The "D" section is not full genomes, but those single sequences from GenBank general release sections, along with refseq, uniprot, genpept databanks. Species genomes: Drosophila_melanogaster [C,G,P,D] Drosophila_yakuba [S,D] Drosophila_simulans [S,D] Drosophila_sechellia [-] Drosophila_ananassae [S,D] Drosophila_erecta [S,D] Drosophila_pseudoobscura [C,G,P,D] Drosophila_persimilis [D] Drosophila_mojavensis [S,D] Drosophila_willistoni [D] Drosophila_virilis [S,D] Drosophila_grimshawi [D] Genome data key: Feature Type choice -------------------------- ------------------------- C = published Chromosomes Chromosomes or Scaffolds S = preliminary assembly Scaffolds; " G = genome Genes; genome Genes P = genome Proteins; genome Proteins - = no data yet D = Databank sequences (NT) from Databank sequences GenBank/EMBL, RefSeq; Databank proteins (AA) Databank proteins from UniProt, RefSeqp, GenPept; Introduction to the Standalone WWW Blast serverIndex
IntroductionThis 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 has 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 and may be done by experienced programmers using source code, which is also provided. Recompilation of the server executables require that programmer has compiled NCBI toolkit libraries. This toolkit can be downloaded from the NCBI FTP web site: ftp://ftp.ncbi.nih.gov What's new in this revision?
Installation of the Standalone WWW serverAfter 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:
Description of files in the distribution
Configuration of BLAST databasesTo set up databases for the standalone WWW BLAST server, it is necessary to follow these steps:
PSI/PHI Blast notesThere 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.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 Client/server version for Entrez lookup and taxonomy reportsRegular 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 info@ncbi.nlm.nih.gov for further assistance.XML outputPossibility 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 blast-help@ncbi.nlm.nih.gov 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 sequencesBlast 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 BlastRPS 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. Out of Frame BLASTXThe 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. Description of tags for the main BLAST input pageThis 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.
Server configuration file and logfileDefault configuration file is "blast.rc" and logfile "wwwblast.log". Setting tag WWW_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.How to debug WWW Blast programsThere is a way to debug these programs.
dbx blast.REAL core and then use command "where" to print stack. BLAST Help Desk Last modified: Fri Jan 11, 2002 |