BLAST - Revision history

Megen002: /* Module file */

2014-03-15T08:55:58Z

Module file

← Older revision		Revision as of 10:55, 15 March 2014
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	== Module file ==		== Module file ==
	The module file can be found in this location:		The module file can be found in this location:
	/cm/shared/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/cm/shared/modulefiles/SHARED/

	<source lang='tcl'>		<source lang='tcl'>
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	module-whatis "Adds blast+ v2.2.28 to your environment"		module-whatis "Adds blast+ v2.2.28 to your environment"

	set blastplus_2228_root /cm/shared/apps/~~WUR/ABGC~~/blast/ncbi-blast-2.2.28+/bin/		set blastplus_2228_root /cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/

	prepend-path PATH $blastplus_2228_root		prepend-path PATH $blastplus_2228_root

Megen002: /* External links */

2013-12-24T20:25:24Z

External links

← Older revision		Revision as of 22:25, 24 December 2013
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	* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast homepage]		* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast homepage]
	* [http://en.wikipedia.org/wiki/BLAST Blast on Wikipedia]		* [http://en.wikipedia.org/wiki/BLAST Blast on Wikipedia]
			* [http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.Cookbook Blast Cookbook]

Megen002: /* Installation details */

2013-12-21T12:18:51Z

Installation details

← Older revision		Revision as of 14:18, 21 December 2013
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	== Installation details ==		== Installation details ==
	Installed from pre-compiled binaries through link on the RepeatMasker homepage.		Installed from pre-compiled binaries through link on the [http://www.repeatmasker.org/RMBlast.html RepeatMasker homepage].

	== See also ==		== See also ==

Megen002 at 12:16, 21 December 2013

2013-12-21T12:16:49Z

← Older revision		Revision as of 14:16, 21 December 2013
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	</source>		</source>

			== Installation details ==
			Installed from pre-compiled binaries through link on the RepeatMasker homepage.

	== See also ==		== See also ==

Megen002: /* See also */

2013-12-21T10:45:39Z

Megen002: /* External links */

2013-12-20T21:16:50Z

External links

← Older revision		Revision as of 23:16, 20 December 2013
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	== External links ==		== External links ==
	* [http://~~www~~.~~yandell-lab~~.~~org~~/~~software/maker~~.~~html Maker~~ homepage]		* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast homepage]
	* [http://~~gmod~~.org/wiki/~~MAKER_Tutorial_2013 Maker tutorial~~]		* [http://en.wikipedia.org/wiki/BLAST Blast on Wikipedia]

Megen002: /* Module file */

2013-12-20T21:15:25Z

Module file

← Older revision		Revision as of 23:15, 20 December 2013
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	</source>		</source>
	Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the <code>TMPDIR</code> environment variable gets set to <code>/local</code>.
	== See also ==		== See also ==

Megen002 at 21:14, 20 December 2013

2013-12-20T21:14:50Z

← Older revision		Revision as of 23:14, 20 December 2013
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	'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''BLAST''', is an [[algorithm]] for comparing ~~[[Primary structure\|~~primary]] biological sequence information, such as the ~~[[amino acid\|~~amino-acid]] sequences of different ~~[[protein]]s~~ or the ~~[[nucleotide]]s~~ of [[DNA ~~sequence]]s~~. A BLAST search enables a researcher to compare a query sequence with a library or [[database]] of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences. For example, following the discovery of a previously unknown gene in the ~~[[Mus musculus\|~~mouse]], a scientist will typically perform a BLAST search of the [[human genome]] to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.		'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''[http://en.wikipedia.org/wiki/BLAST BLAST]''', is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.

	== Module file ==		== Module file ==

Megen002: Created page with "'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''BLAST''', is an algorithm for comparing primary biological sequence informatio..."

2013-12-20T21:12:35Z

Created page with "'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''BLAST''', is an algorithm for comparing primary biological sequence informatio..."

New page

'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''BLAST''', is an [[algorithm]] for comparing [[Primary structure|primary]] biological sequence information, such as the [[amino acid|amino-acid]] sequences of different [[protein]]s or the [[nucleotide]]s of [[DNA sequence]]s. A BLAST search enables a researcher to compare a query sequence with a library or [[database]] of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences. For example, following the discovery of a previously unknown gene in the [[Mus musculus|mouse]], a scientist will typically perform a BLAST search of the [[human genome]] to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.

== Module file ==
The module file can be found in this location:
/cm/shared/apps/WUR/ABGC/modulefiles

<source lang='tcl'>
#%Module1.0#######################################################################
## BLAST+ 2.2.28 modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds blast+ v2.2.28 to your environment"
}

module-whatis "Adds blast+ v2.2.28 to your environment"

set blastplus_2228_root /cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/

prepend-path PATH $blastplus_2228_root

</source>
Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the <code>TMPDIR</code> environment variable gets set to <code>/local</code>.
== See also ==

== External links ==
* [http://www.yandell-lab.org/software/maker.html Maker homepage]
* [http://gmod.org/wiki/MAKER_Tutorial_2013 Maker tutorial]

← Older revision		Revision as of 12:45, 21 December 2013
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	== See also ==		== See also ==
			* [[Globally_installed_software \| Globally installed software]]
			* [[ABGC_modules \| ABGC specific modules]]

	== External links ==		== External links ==
	* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast homepage]		* [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast homepage]
	* [http://en.wikipedia.org/wiki/BLAST Blast on Wikipedia]		* [http://en.wikipedia.org/wiki/BLAST Blast on Wikipedia]