Difference between revisions of "Web based genome comparison tool"

Revision as of 15:42, 22 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
  - 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

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)

@@ 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]