Difference between revisions of "Web based genome comparison tool"

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**in C and Python
 
**in C and Python
 
**Runs locally from command line??? => could generate on server. Too much work for server?
 
**Runs locally from command line??? => could generate on server. Too much work for server?
−
*[http://www.broadinstitute.org/annotation/medea/dotplot/ MEDEA]
+
*[http://www.broadinstitute.org/annotation/medea/dotplot/ Dotplot MEDEA]
 
**This is what I want!
 
**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.
 
**At its minimum, the MEDEA Dot Plot only needs JSON formatted data for the sequences and JSON formatted data for alignments.
−
*[http://www.broadinstitute.org/annotation/medea/stackmap/]
+
**Need to calculate alignments
 +
***http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html
 +
***>>> import Bio.Align.Applications >>> dir(Bio.Align.Applications)
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***from Bio.Emboss.Applications import NeedleCommandline
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*[http://www.broadinstitute.org/annotation/medea/stackmap/ Multi MEDIA]
 
**Multigenome comparison tool
 
**Multigenome comparison tool
 +
*[http://www.jalview.org/index.html Jalview]
 +
**Kinda like clustalW
 +
 +
==For Computation==
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*[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]
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*[http://mugsy.sourceforge.net/ MUGSY]
 +
**[http://bioinformatics.oxfordjournals.org/content/early/2010/12/09/bioinformatics.btq665.full.pdf publication]
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**Most recently released... claims to be comparable but faster than other alignment tools.
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**Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)]
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<pre>
 +
Parsing sequences for seq1  num_seqs:30
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Parsing sequences for seq2  num_seqs:30
 +
2 genomes
 +
Starting Nucmer: Mon Sep 26 13:35:28 EDT 2011
 +
.
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Finished Nucmer Mon Sep 26 13:35:28 EDT 2011
 +
Starting MUGSYWGA: Mon Sep 26 13:35:28 EDT 2011
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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.
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</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...
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**compile library files...
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***gcc -c -Wall -O2 file1.c
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**get info on .a file
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***lipo -info /usr/local/projects/angiuoli/mugsy_trunk/maflib/libmaf.a
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**make .a file
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***ar rcs libmaf.a mz_scores.o charvec.o nib.o seq.o multi_util.o maf.o util.o
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***ranlib libmaf.a
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**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.
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