Difference between revisions of "Web based genome comparison tool"

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(For Computation)
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**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)]
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Parsing sequences for seq1  num_seqs:30
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Parsing sequences for seq2  num_seqs:30
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2 genomes
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Starting Nucmer: Mon Sep 26 13:35:28 EDT 2011
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.
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Finished Nucmer Mon Sep 26 13:35:28 EDT 2011
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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.

Revision as of 17:36, 26 September 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.