Blast - Revision history

PeterThorpe: added blast databases with tax db.

2018-10-23T13:57:14Z

added blast databases with tax db.

Rf at 16:18, 1 February 2016

2016-02-01T16:18:09Z

Rf at 16:17, 1 February 2016

2016-02-01T16:17:36Z

Rf at 14:59, 1 February 2016

2016-02-01T14:59:20Z

Rf at 14:46, 1 February 2016

2016-02-01T14:46:05Z

Rf: Created page with "=Introduction= The workhorse of bioinformatics, some tips on usgae, and (mostly) how to speed it up = Benchmark Exercises = == Transcriptome Panda Blood == * 92600 transcri..."

2016-02-01T14:07:40Z

Created page with "=Introduction= The workhorse of bioinformatics, some tips on usgae, and (mostly) how to speed it up = Benchmark Exercises = == Transcriptome Panda Blood == * 92600 transcri..."

New page

=Introduction=
The workhorse of bioinformatics, some tips on usgae, and (mostly) how to speed it up

= Benchmark Exercises =

== Transcriptome Panda Blood ==

* 92600 transcripts (contigs) in 2.4 million line FASTA file.
* blastx speed on 62-fragmented nr database: 5% of contigs in 33 hours on blastx

← Older revision		Revision as of 13:57, 23 October 2018
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	The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up		The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up
		+
		+
		+	== BLAST ==
		+
		+
		+	READ this for how to run blast: https://www.ncbi.nlm.nih.gov/books/NBK279680/
		+
		+	http://nebc.nerc.ac.uk/bioinformatics/documentation/blast+/user_manual.pdf
		+
		+
		+	# Put this in your script or in your .bash_profile
		+	export BLASTDB=/shelf/public/blastntnr/blastDatabases
		+
		+	# to add the latest BLAST tools to you path
		+	export PATH=/shelf/apps/ncbi-blast-2.7.1+/bin/:$PATH
		+
		+	# now you can run against nr , nt , human_genomic, uniprot_sprot.fasta:
		+	> blastp -db '''nr''' -query amino_acid.fasta -out tests.txt
		+
		+	Taxonomy database is also in here: /shelf/public/blastntnr/blastDatabases. So if you want the extended BLAST format, this should just work, assuming you ask for it.
		+
		+	== FULL EXAMPLE: ==
		+	export BLASTDB=/shelf/public/blastntnr/blastDatabases
		+
		+	export PATH=/shelf/apps/ncbi-blast-2.7.1+/bin/:$PATH
		+
		+	blastp -db nr -query MY_AA.fasta -evalue 1e-5 -seg no -num_threads 8 -outfmt "6 std salltitles staxids sscinames scomnames sskingdoms" -out MY_AA_vs_nr.fa_NR_18oct2018.tab
		+
		+

	= Output formats =		= Output formats =

@@ Line 9: / Line 9: @@
 This is for the old blast and mpiblast
-* Query id
+# Query id
-* Subject id
+# Subject id
-* % identity
+# % identity
-* alignment length
+# alignment length
-* mismatches
+# mismatches
-* gap openings
+# gap openings
-* q. start
+# q. start
-* q. end
+# q. end
-* s. start
+# s. start
-* s. end
+# s. end
-* e-value
+# e-value
-* bit score
+# bit score
 = Benchmark Exercises =

← Older revision		Revision as of 14:59, 1 February 2016
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	* 92600 transcripts (contigs) in 2.4 million line FASTA file.		* 92600 transcripts (contigs) in 2.4 million line FASTA file.
−	* blastx speed on 62-fragmented nr database: 5% of contigs in 33 hours on blastx	+	* blastx speed on 62-fragmented nr database: 5% (about 4500 contigs then) in 33 hours on blastx

@@ Line 1: / Line 1: @@
 =Introduction=
 The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up
 = Benchmark Exercises =