Difference between revisions of "Web based genome comparison tool"
From GcatWiki
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**[http://bioinformatics.oxfordjournals.org/content/early/2010/12/09/bioinformatics.btq665.full.pdf publication] | **[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. | **Most recently released... claims to be comparable but faster than other alignment tools. | ||
| − | **Output = Multiple Alignment Format (MAF) | + | **Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)] |
Revision as of 15:49, 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
For Computation
- TBA (Threaded Blockset Aligner)
- MUGSY
- publication
- Most recently released... claims to be comparable but faster than other alignment tools.
- Output = Multiple Alignment Format (MAF)
