Difference between revisions of "Web based genome comparison tool"

From GcatWiki
Jump to: navigation, search
(Created page with '*[http://www.jxxi.com/webstart/app/jdotter-a-java-dot-plot-viewer.html JDotter] **A java based tool designed to compare whole genome **Runs comparison operations locally **Need a…')
 
(→‎For Computation)
 
(20 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
**Runs comparison operations locally
 
**Runs comparison operations locally
 
**Need a java install thing
 
**Need a java install thing
 +
*[https://docs.google.com/viewer?url=http%3A%2F%2Fwww.iscb.org%2Fcms_addon%2Fconferences%2Fismb2005%2Fdemos%2F30.pdf M-GCAT]
 +
**in C and Python
 +
**Runs locally from command line??? => could generate on server. Too much work for server?
 +
*[http://www.broadinstitute.org/annotation/medea/dotplot/ Dotplot MEDEA]
 +
**This is what I want!
 +
**At its minimum, the MEDEA Dot Plot only needs JSON formatted data for the sequences and JSON formatted data for alignments.
 +
**Need to calculate alignments
 +
***http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html
 +
***>>> import Bio.Align.Applications >>> dir(Bio.Align.Applications)
 +
***from Bio.Emboss.Applications import NeedleCommandline
 +
*[http://www.broadinstitute.org/annotation/medea/stackmap/ Multi MEDIA]
 +
**Multigenome comparison tool
 +
*[http://www.jalview.org/index.html Jalview]
 +
**Kinda like clustalW
 +
 +
==For Computation==
 +
*[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]
 +
**[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 = [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
 +
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.
 +
</pre>
 +
*Issues with mugsy
 +
**When use --duplications command, no matter what it is set, a file ______10_16.filt.delta is not deleted
 +
**When use --duplications 1 command, that file and 1error.dups.maf is present.
 +
 +
* 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
 +
**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

Latest revision as of 21:20, 13 October 2011

  • JDotter
    • A java based tool designed to compare whole genome
    • Runs comparison operations locally
    • Need a java install thing
  • M-GCAT
    • in C and Python
    • Runs locally from command line??? => could generate on server. Too much work for server?
  • Dotplot MEDEA
    • This is what I want!
    • At its minimum, the MEDEA Dot Plot only needs JSON formatted data for the sequences and JSON formatted data for alignments.
    • Need to calculate alignments
  • Multi MEDIA
    • Multigenome comparison tool
  • Jalview
    • Kinda like clustalW

For Computation

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.
  • Issues with mugsy
    • When use --duplications command, no matter what it is set, a file ______10_16.filt.delta is not deleted
    • When use --duplications 1 command, that file and 1error.dups.maf is present.
Retrieved from "https://gcat.davidson.edu/GcatWiki/index.php?title=Web_based_genome_comparison_tool&oldid=13571"