Parsing Blast Results from Your Favorite Database - Revision history

Letaylor at 22:46, 23 February 2011

2011-02-23T22:46:21Z

2011-02-23T21:06:57Z

2011-02-23T21:06:42Z

2011-02-23T21:06:32Z

2011-02-23T21:05:38Z

2011-02-23T20:45:52Z

2011-02-23T20:44:25Z

2011-02-23T20:41:42Z

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2011-02-23T20:36:42Z

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 #Download [http://dl.dropbox.com/u/4936834/blastparse.py blastParse.py]
 #Place blastParse.py into the same folder as your blast results file
-#In terminal, navigate into the folder containing blastParse.py, and your blast results file
+#In terminal, navigate into the folder containing blastParse.py and your blast results file
 #Run blastParse.py using the command <pre>python blastParse.py</pre>
 #Follow prompts of the BLASTPARSE program

← Older revision		Revision as of 21:06, 23 February 2011
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−	A video of this tutorial can be found [~~here~~ http://megaswf.com/serve/1028117].	+	A video of this tutorial can be found [http://megaswf.com/serve/1028117 here].

@@ Line 16: / Line 16: @@
 #Follow prompts of the BLASTPARSE program
 #Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).
 A video of this tutorial can be found [here http://megaswf.com/serve/1028117].

← Older revision		Revision as of 21:06, 23 February 2011
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	#Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).		#Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).

−	~~<iframe frameborder="0" scrolling="no" src="" id="megaswf"></iframe><script src="~~http://megaswf.com/~~ServeEmbedJS~~.~~aspx?fileID=1028117&height=1049&width=1679&iframeID=megaswf" type="text/javascript"></script>~~	+	A video of this tutorial can be found [here http://megaswf.com/serve/1028117].

← Older revision		Revision as of 21:05, 23 February 2011
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	#Follow prompts of the BLASTPARSE program		#Follow prompts of the BLASTPARSE program
	#Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).		#Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).
		+
		+	<iframe frameborder="0" scrolling="no" src="" id="megaswf"></iframe><script src="http://megaswf.com/ServeEmbedJS.aspx?fileID=1028117&height=1049&width=1679&iframeID=megaswf" type="text/javascript"></script>

@@ Line 3: / Line 3: @@
 NOTE: This tutorial assumes the user has blast version 2.2.24 installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.
-#Run your search using the command<pre>/usr/local/ncbi/blast/bin/blastn -query querySequence.fasta -db dataBase.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" -out blast_output.txt</pre>
+#Open terminal and navigate into the folder containing the blast query sequence and the blast data base using following Unix commands<pre>cd OR ls</pre>
 #:What does this command do? "-" indicates a command. The text that follows is the actual command parameters.
 #:*-query = query file
@@ Line 11: / Line 12: @@
 #Download [http://dl.dropbox.com/u/4936834/blastparse.py blastParse.py]
 #Place blastParse.py into the same folder as your blast results file
-#Open terminal and navigate into the folder containing blastParse.py using following Unix commands<pre>cd OR ls</pre>
+#Open terminal and navigate into the folder containing blastParse.py
 #Run blastParse.py using the command <pre>python blastParse.py</pre>
 #Follow prompts of the BLASTPARSE program
 #Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (''right click'' > open with > excel).

← Older revision		Revision as of 20:41, 23 February 2011
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	This tutorial demonstrates how to quickly parse out hits from a '''blastn''' search on a local blast database. A python script ([http://dl.dropbox.com/u/4936834/blastparse.py blastParse.py]) is used to parse the data. This script was developed to identify what pieces of an unfinished blueberry genome (scaffold/contig) typically had the most instances of chloroplasts or mitochondrial DNA.		This tutorial demonstrates how to quickly parse out hits from a '''blastn''' search on a local blast database. A python script ([http://dl.dropbox.com/u/4936834/blastparse.py blastParse.py]) is used to parse the data. This script was developed to identify what pieces of an unfinished blueberry genome (scaffold/contig) typically had the most instances of chloroplasts or mitochondrial DNA.
−

	NOTE: This tutorial assumes the user has blast version 2.2.24 installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.		NOTE: This tutorial assumes the user has blast version 2.2.24 installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.

← Older revision		Revision as of 20:36, 23 February 2011
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−	This tutorial demonstrates how to ~~isolate data~~ from ~~large~~ blast ~~hits~~.	+	This tutorial demonstrates how to quickly parse out hits from a '''blastn''' search on a local blast database.

	NOTE: This tutorial assumes the user has blast version 2.2.24 installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.		NOTE: This tutorial assumes the user has blast version 2.2.24 installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.