BLAST - Revision history

Christoph at 22:12, 9 July 2012

2012-07-09T22:12:52Z

Christoph: /* Blast Family of Programs */

2012-07-05T17:01:55Z

‎Blast Family of Programs

Christoph: /* Format your BLAST database files */

2012-07-05T15:47:08Z

‎Format your BLAST database files

Christoph at 19:00, 17 February 2012

2012-02-17T19:00:22Z

Christoph: /* External links */

2009-04-15T02:06:58Z

‎External links

Christoph: /* See also */

2009-04-15T01:58:29Z

‎See also

Christoph: /* Overview of database search programs */

2009-02-07T03:43:55Z

‎Overview of database search programs

Christoph: /* Standalone BLAST tools and utilities */

2009-02-07T03:43:33Z

‎Standalone BLAST tools and utilities

Christoph: /* External links */

2008-05-15T22:14:52Z

‎External links

Christoph at 21:41, 15 May 2008

2008-05-15T21:41:15Z

@@ Line 5: / Line 5: @@
 The latest stable version is: '''2.2.25''' (2011-03-31)
-  see also: [[formatdb]], [[BLAST/matrices]]
+  see also: [[BLAST+]], [[formatdb]], [[BLAST/matrices]]
 ==Installation==

@@ Line 101: / Line 101: @@
 ==Blast Family of Programs==
 The BLAST family of programs allows all combinations of DNA or protein query sequences with searches against DNA or protein databases:
-;<tt>blastp</tt>: compares an amino acid query sequence against a protein sequence database.
+;<tt>blastp</tt>: compares an ''amino acid'' query sequence against a ''protein'' sequence database.
-;<tt>blastn</tt>: compares a nucleotide query sequence against a nucleotide sequence database.
+;<tt>blastn</tt>: compares a ''nucleotide'' query sequence against a ''nucleotide'' sequence database.
-;<tt>blastx</tt>: compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
+;<tt>blastx</tt>: compares the six-frame conceptual translation products of a ''nucleotide'' query sequence (both strands) against a ''protein'' sequence database.
-;<tt>tblastn</tt>: compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
+;<tt>tblastn</tt>: compares a ''protein'' query sequence against a ''nucleotide'' sequence database dynamically translated in all six reading frames (both strands).
-;<tt>tblastx</tt>: compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
+;<tt>tblastx</tt>: compares the six-frame translations of a ''nucleotide'' query sequence against the six-frame translations of a ''nucleotide'' sequence database.
-The default matrix for all protein-protein comparisons is BLOSUM62.
+Note: The default matrix for all protein-protein comparisons is BLOSUM62.
 ==Databases available for BLAST search==

@@ Line 54: / Line 54: @@
 </pre>
-To run the first search enter the following command from the Linux command line in your BLAST directory:
+To run your first (test) search, enter the following command from the Linux command line in your BLAST directory:
   blastall -p blastn -d ecoli.nt -i test.txt -o test.out
 This should generate a results file called <code>test.out</code> in the Standalone BLAST directory.
-Now you are ready to create your own databases and run BLAST searches. For more information you should refer to the Standalone BLAST README (ftp://ftp.ncbi.nih.gov/blast/executable/) and the BLAST literature. This will give you some idea of all the programs BLAST supports and the use of different parameters for increasing or decreasing the stringency of your results.
+Now you are ready to create your own databases and run BLAST searches. For more information, you should refer to the Standalone BLAST README (ftp://ftp.ncbi.nih.gov/blast/executable/) and the BLAST literature. This will give you some idea of all the programs BLAST supports and the use of different parameters for increasing or decreasing the stringency of your results.
 ==Standalone BLAST tools and utilities==

@@ Line 3: / Line 3: @@
 It is a service of the National Center for Biotechnology Information (NCBI). A nucleotide or protein sequence sent to the BLAST server is compared against databases at the NCBI and a summary of matches is returned to the user.
-The latest stable version is: '''2.2.18''' (2008-03-21)
+The latest stable version is: '''2.2.25''' (2011-03-31)
   see also: [[formatdb]], [[BLAST/matrices]]
 ==Installation==
-''Note: The following is based on the "README for stand-alone BLAST" document. It will only cover the process for [[Linux]] systems.''
+''Note: The following is based on the "README for stand-alone BLAST" document. It will only cover the process for [[Linux]] systems (and assume 32-bit OS).''
 ===Download===
-Download the latest version of BLAST for Linux from ftp://ftp.ncbi.nih.gov/blast/ (the archive will be called something like <code>blast-2.2.16-ia32-linux.tar.gz</code>).
+Download the latest version of BLAST for Linux from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ (the archive will be called something like <code>ncbi-blast-2.2.25+-ia32-linux.tar.gz</code> for 32-bit versions).
 ===Configuration file===
@@ Line 25: / Line 25: @@
 ===Format your BLAST database files===
-The main advantage of Standalone BLAST is to be able to create your own BLAST databases. This can be done with any file of FASTA formatted protein or nucleotide sequences. If you are interested in creating your own database files you should refer to the sections "Non-redundant defline syntax" and "Appendix 1: Sequence Identifier Syntax" of the README in the BLAST database directory
+The main advantage of Standalone BLAST is to be able to create your own BLAST databases. This can be done with any file of FASTA formatted protein or nucleotide sequences. If you are interested in creating your own database files you should refer to the sections "Non-redundant defline syntax" and "Appendix 1: Sequence Identifier Syntax" of the README in the BLAST database directory (ftp://ftp.ncbi.nih.gov/blast/db/). You can also refer to the FASTA description available from the BLAST search pages (http://www.ncbi.nlm.nih.gov/BLAST/fasta.html).
 (ftp://ftp.ncbi.nih.gov/blast/db/). You can also refer to the FASTA description available from the BLAST search pages (http://www.ncbi.nlm.nih.gov/BLAST/fasta.html).
 However, for a testing purposes you should download one of the NCBI databases and run a search against it.

@@ Line 216: / Line 216: @@
 *[http://www.genome.jp/en/info_dbget.html DBGET - release info]
 *[http://books.google.com/books?id=xvcnhDG9fNUC O'Reilly BLAST book on Google Books]
 [[Category:Bioinformatics]]

@@ Line 203: / Line 203: @@
 *[[FASTA format]]
 *[http://bioinfo.iq.usp.br/zerg/ The Zerg BLAST Parser]
 ==References==

@@ Line 143: / Line 143: @@
 |}
 </div>
 ==Database updates==

@@ Line 65: / Line 65: @@
 ;bl2seq: performs a comparison between two sequences using either the blastn or blastp algorithm. Both sequences must be either nucleotides or proteins.
 ;[[blastall]]: may be used to perform all five flavors of blast comparison.
-;blastclust: automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA.
+;[http://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html blastclust]: automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA.
 ;blastpgp: performs gapped blastp searches and can be used to perform iterative searches in psi-blast and phi-blast mode.
 ;copymat: copy matrices
@@ Line 75: / Line 75: @@
 ;megablast: uses a greedy algorithm for nucleotide sequence alignment search and concatenates many queries to save time spent scanning the database.
 ;rpsblast: (Reverse PSI-BLAST) searches a query sequence against a database of profiles.
 ;seedtop:
 ==BLAST Assembled Genomes==