Web based genome comparison tool

• 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
    • http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html
    • >>> import Bio.Align.Applications >>> dir(Bio.Align.Applications)
    • from Bio.Emboss.Applications import NeedleCommandline
• Multi MEDIA
  • Multigenome comparison tool
• Jalview
  • Kinda like clustalW

For Computation

• TBA (Threaded Blockset Aligner)
  • documentation and publication
• MUGSY
  • publication
  • Most recently released... claims to be comparable but faster than other alignment tools.
  • Output = 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.

• 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