Wikiomics:BLAST tutorial - Revision history

Darek Kedra: /* Mitrion-C for BLAST */ delete: company went down

2011-05-04T12:28:27Z

Mitrion-C for BLAST: delete: company went down

←Older revision		Revision as of 12:28, 4 May 2011
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	http://www.progeniq.com/		http://www.progeniq.com/

-	~~==Mitrion-C for BLAST==~~	+
-	~~Open source implementation (not complete)~~	+
-	~~http://mitc-openbio.sourceforge.net/blast_docs.html~~	+

	==Other efforts==		==Other efforts==

2011-03-01T17:20:06Z

pre tag

←Older revision		Revision as of 17:20, 1 March 2011
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	This tutorial covers previous version of blast (blastall). The newest BLAST+ tools use NCBI C++ Toolkit and offer new functionality not covered here.		This tutorial covers previous version of blast (blastall). The newest BLAST+ tools use NCBI C++ Toolkit and offer new functionality not covered here.
-	For detailed help on command line blastall switches type: blastall --help	+	For detailed help on command line blastall switches type:
-		+	<pre>
		+	blastall --help
		+	</pre>
	Download blast searches results from [http://openwetware.org/wiki/Image:Blast_course_080208.zip here]		Download blast searches results from [http://openwetware.org/wiki/Image:Blast_course_080208.zip here]

2011-03-01T17:17:50Z

WU-BLAST / AB-BLAST

←Older revision		Revision as of 17:17, 1 March 2011
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	* http://blast.wustl.edu/		* http://blast.wustl.edu/

-	Program was licensed to [http://www.advbiocomp.com/blast.html Advanced Biocomputing] and becoming AB-BLAST. Previous licenses are still valid, but WU-BLAST versions except an obsolete 2.0a19 from 1998 are unavailable. ~~As for Feb 12th 2010 latest~~ AB-BLAST version is 2009-10-30. Licensing is [http://blast.advbiocomp.com/licensing/ here] (1k$ /year/lab, free for personal use on your own computer).	+	Program was licensed to [http://www.advbiocomp.com/blast.html Advanced Biocomputing] and becoming AB-BLAST. Previous licenses are still valid, but WU-BLAST versions except an obsolete 2.0a19 from 1998 are unavailable. Latest AB-BLAST version is 2009-10-30. Licensing is [http://blast.advbiocomp.com/licensing/ here] (1k$ /year/lab, free for personal use on your own computer).

	==MPI-BLAST==		==MPI-BLAST==

2011-02-12T14:36:25Z

←Older revision		Revision as of 14:36, 12 February 2011
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	blastall -p blastp -d ecoli_aa -i my_nn_fasta_file.fa -o my_nn_fasta_file_vs_ecolidb.blastp_out		blastall -p blastp -d ecoli_aa -i my_nn_fasta_file.fa -o my_nn_fasta_file_vs_ecolidb.blastp_out
	</pre>		</pre>
		+
		+	=Non-command line BLAST=
		+	BLAST can be setup to be queried using an internet browser instead of a command line, using NCBI's [[wwwblast]] software. The command line must be used during the setup of wwwblast, but not when running the actual BLAST queries.

	=Advanced topics=		=Advanced topics=

2010-09-29T16:02:40Z

Filtering blast output using Entrez query

←Older revision		Revision as of 16:02, 29 September 2010
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	<pre>		<pre>
	blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt		blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt
		+	</pre>
		+
		+	This can also be written as:
		+	<pre>
		+	blastall -u "txid3702[ORGN]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt
	</pre>		</pre>

2010-09-29T15:38:03Z

Filters and Masking

←Older revision		Revision as of 15:38, 29 September 2010
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	* custom filtering (lower case masking)		* custom filtering (lower case masking)
	By providing query sequence i.e. genomic sequence with '''EXONS''' as capitals and '''introns''' in small letters we can search exonic sequences only.		By providing query sequence i.e. genomic sequence with '''EXONS''' as capitals and '''introns''' in small letters we can search exonic sequences only.
		+
		+	==Filtering blast output using Entrez query==
		+	One can be interested only in blast hits from i.e. specific organism. On a command line:
		+	<pre>
		+	blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt
		+	</pre>

	=BLAST implementations=		=BLAST implementations=

2010-09-01T10:39:13Z

CS-BLAST

←Older revision		Revision as of 10:39, 1 September 2010
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	* http://toolkit.lmb.uni-muenchen.de/cs_blast		* http://toolkit.lmb.uni-muenchen.de/cs_blast

-	Biegert, A. and Soding, J. (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA, 106 (10), 3770-3775	+	Biegert, A. and Soding, J. (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA, 106 (10), 3770-3775

		+	Latest version: 2.1.0 from 2009-08-17

	==FSA-BLAST==		==FSA-BLAST==

2010-09-01T10:37:21Z

ScalaBLAST

←Older revision		Revision as of 10:37, 1 September 2010
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	==ScalaBLAST==		==ScalaBLAST==
-	Novel implementation	+	Novel implementation for clusters, requires MPI.
	* http://hpc.pnl.gov/projects/scalablast/		* http://hpc.pnl.gov/projects/scalablast/
		+
		+	Latest version: 1.0.640 from 2010-04-05

	==CS-BLAST==		==CS-BLAST==

2010-09-01T10:33:29Z

MPI-BLAST

←Older revision		Revision as of 10:33, 1 September 2010
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	==MPI-BLAST==		==MPI-BLAST==
-	BLAST implementation suitable for clusters	+	BLAST implementation suitable for clusters, under active development.
	* http://www.mpiblast.org/		* http://www.mpiblast.org/
		+
		+	Latest version: mpiBLAST-1.6.0 from 2010-07-13.

	==ScalaBLAST==		==ScalaBLAST==

2010-03-20T19:49:33Z

Mitrion-C for BLAST

←Older revision		Revision as of 19:49, 20 March 2010
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	http://mitc-openbio.sourceforge.net/blast_docs.html		http://mitc-openbio.sourceforge.net/blast_docs.html

-	Other efforts ~~include:~~	+	==Other efforts==
	* Mercury BLASTP		* Mercury BLASTP
	* CAAD BLASTP		* CAAD BLASTP