Web based genome comparison tool - Revision history

Letaylor: /* For Computation */

2011-10-13T21:20:41Z

‎For Computation

2011-10-13T15:39:31Z

‎For Computation

2011-10-03T17:33:32Z

‎For Computation

2011-09-26T17:37:10Z

‎For Computation

2011-09-26T17:37:00Z

‎For Computation

2011-09-26T17:36:23Z

‎For Computation

2011-09-22T16:07:18Z

2011-09-22T15:49:09Z

‎For Computation

2011-09-22T15:42:15Z

‎For Computation

2011-09-22T15:41:53Z

‎For Computation

@@ Line 35: / Line 35: @@
 system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30  --unique true  > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.
 </pre>
+*Issues with mugsy
 * stuff learned from building mugsy...

← Older revision		Revision as of 15:39, 13 October 2011
Line 45:		Line 45:
	***ar rcs libmaf.a mz_scores.o charvec.o nib.o seq.o multi_util.o maf.o util.o		***ar rcs libmaf.a mz_scores.o charvec.o nib.o seq.o multi_util.o maf.o util.o
	***ranlib libmaf.a		***ranlib libmaf.a
		+	**make lbgl-viz http://www.cs.brown.edu/~jwicks/boost/libs/graph/doc/read-graphviz.html and http://lists.boost.org/boost-users/2006/04/18680.php

← Older revision		Revision as of 17:33, 3 October 2011
Line 35:		Line 35:
	system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30 --unique true > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.		system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30 --unique true > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.
	</pre>		</pre>
		+
		+
		+	* stuff learned from building mugsy...
		+	**compile library files...
		+	***gcc -c -Wall -O2 file1.c
		+	**get info on .a file
		+	***lipo -info /usr/local/projects/angiuoli/mugsy_trunk/maflib/libmaf.a
		+	**make .a file
		+	***ar rcs libmaf.a mz_scores.o charvec.o nib.o seq.o multi_util.o maf.o util.o
		+	***ranlib libmaf.a

← Older revision		Revision as of 17:37, 26 September 2011
Line 34:		Line 34:
	Starting MUGSYWGA: Mon Sep 26 13:35:28 EDT 2011		Starting MUGSYWGA: Mon Sep 26 13:35:28 EDT 2011
	system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30 --unique true > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.		system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30 --unique true > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.
		+	</pre>

@@ Line 25: / Line 25: @@
 **Most recently released... claims to be comparable but faster than other alignment tools.
 **Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)]
+<pre>
 Parsing sequences for seq1  num_seqs:30
 Parsing sequences for seq2  num_seqs:30

← Older revision		Revision as of 17:36, 26 September 2011
Line 25:		Line 25:
	**Most recently released... claims to be comparable but faster than other alignment tools.		**Most recently released... claims to be comparable but faster than other alignment tools.
	**Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)]		**Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)]
		+
		+	Parsing sequences for seq1 num_seqs:30
		+	Parsing sequences for seq2 num_seqs:30
		+	2 genomes
		+	Starting Nucmer: Mon Sep 26 13:35:28 EDT 2011
		+	.
		+	Finished Nucmer Mon Sep 26 13:35:28 EDT 2011
		+	Starting MUGSYWGA: Mon Sep 26 13:35:28 EDT 2011
		+	system /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsyWGA --outfile /Users/letaylor/Desktop/test/test --seq /Users/letaylor/Desktop/test/test.all.fsa --aln /Users/letaylor/Desktop/test/test.xmfa --distance 1000 --minlength 30 --unique true > /Users/letaylor/Desktop/test/test.mugsywga.out 2> /Users/letaylor/Desktop/test/test.mugsywga.stderr failed: 32256: at /Users/letaylor/mugsy_trunk/mugsy_x86-64-v1r2.1/mugsy line 933.

@@ Line 15: / Line 15: @@
 *[http://www.broadinstitute.org/annotation/medea/stackmap/ Multi MEDIA]
 **Multigenome comparison tool
 ==For Computation==

@@ Line 22: / Line 22: @@
 **[http://bioinformatics.oxfordjournals.org/content/early/2010/12/09/bioinformatics.btq665.full.pdf publication]
 **Most recently released... claims to be comparable but faster than other alignment tools.
-**Output = Multiple Alignment Format (MAF)
+**Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)]

@@ Line 17: / Line 17: @@
 ==For Computation==
-*[http://www.bx.psu.edu/miller_lab/dist/multiz-tba.012109.tar.gz TBA]
+*[http://www.bx.psu.edu/miller_lab/dist/multiz-tba.012109.tar.gz TBA (Threaded Blockset Aligner)]
 **[http://bio.cse.psu.edu/dist/tba.pdf documentation] and [http://bio.cse.psu.edu/dist/tba.pdf publication]
 *[http://mugsy.sourceforge.net/ MUGSY]

← Older revision		Revision as of 15:41, 22 September 2011
Line 21:		Line 21:
	*[http://mugsy.sourceforge.net/ MUGSY]		*[http://mugsy.sourceforge.net/ MUGSY]
	**[http://bioinformatics.oxfordjournals.org/content/early/2010/12/09/bioinformatics.btq665.full.pdf publication]		**[http://bioinformatics.oxfordjournals.org/content/early/2010/12/09/bioinformatics.btq665.full.pdf publication]
		+	**Most recently released... claims to be comparable but faster than other alignment tools.
		+	**Output = Multiple Alignment Format (MAF)