Blat v35 - Revision history

Megen002: /* Module file */

2014-03-15T08:56:55Z

Module file

← Older revision		Revision as of 10:56, 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 the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment"		module-whatis "Adds the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment"

	set blat_root /cm/shared/apps/~~WUR/ABGC~~/blat/blat-v35/blat		set blat_root /cm/shared/apps/SHARED/blat/blat-v35/blat
	set blat_tools_root /cm/shared/apps/~~WUR/ABGC~~/blat/blat-v35		set blat_tools_root /cm/shared/apps/SHARED/blat/blat-v35
	prepend-path PATH $blat_tools_root		prepend-path PATH $blat_tools_root
	prepend-path PATH $blat_root		prepend-path PATH $blat_root

2013-12-21T12:15:39Z

Installation details

← Older revision		Revision as of 14:15, 21 December 2013
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	rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./		rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
	</source>		</source>


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

2013-12-21T12:15:31Z

2013-12-21T12:14:31Z

← Older revision		Revision as of 14:14, 21 December 2013
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	'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.		'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.


	~~The entire suite of binaries/executable was downloaded on 20-12-2013:~~
	~~<source lang='bash'>~~
	~~rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./~~
	~~</source>~~

	== Module file ==		== Module file ==
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	</source>		</source>

			== Installation details ==

			The entire suite of binaries/executable was downloaded on 20-12-2013:
			<source lang='bash'>
			rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
			</source>


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

2013-12-20T22:11:24Z

← Older revision		Revision as of 00:11, 21 December 2013
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	The entire suite of binaries/executable was downloaded on 20-12-2013:		The entire suite of binaries/executable was downloaded on 20-12-2013:
	<source lang='bash'>		<source lang='bash'>
	rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ .		rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
	</source>		</source>

2013-12-20T22:01:38Z

External links

← Older revision		Revision as of 00:01, 21 December 2013
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	== External links ==		== External links ==
	* [http://~~blast~~.~~ncbi~~.~~nlm.nih.gov~~/~~Blast~~.~~cgi Blast homepage~~]		* [http://genome.ucsc.edu/FAQ/FAQblat.html Blat at UCSC]
	* [http://en.~~wikipedia~~.~~org~~/~~wiki~~/~~BLAST Blast on Wikipedia~~]		* [http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Download page of 64-bit executables for Linux]

2013-12-20T21:59:37Z

Module file

← Older revision		Revision as of 23:59, 20 December 2013
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	'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.		'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.

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

	The entire suite of binaries/executable was downloaded on 20-12-2013:		The entire suite of binaries/executable was downloaded on 20-12-2013:
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	rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ .		rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ .
	</source>		</source>

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

	<source lang='tcl'>		<source lang='tcl'>

2013-12-20T21:59:03Z

Module file

← Older revision		Revision as of 23:59, 20 December 2013
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	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/apps/WUR/ABGC/modulefiles

			The entire suite of binaries/executable was downloaded on 20-12-2013:
			<source lang='bash'>
			rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ .
			</source>

	<source lang='tcl'>		<source lang='tcl'>

2013-12-20T21:55:50Z

← Older revision		Revision as of 23:55, 20 December 2013
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	'''[[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) \| BLAT]]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.		'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.

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

2013-12-20T21:55:37Z

← Older revision		Revision as of 23:55, 20 December 2013
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	'''~~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~~.		'''[[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) \| BLAT]]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.

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

← Older revision		Revision as of 14:15, 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://genome.ucsc.edu/FAQ/FAQblat.html Blat at UCSC]		* [http://genome.ucsc.edu/FAQ/FAQblat.html Blat at UCSC]
	* [http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Download page of 64-bit executables for Linux]		* [http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Download page of 64-bit executables for Linux]