Difference between revisions of "Web based genome comparison tool"
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**Need to calculate alignments | **Need to calculate alignments | ||
***http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html | ***http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html | ||
| − | ***>>> import Bio.Align.Applications | + | ***>>> import Bio.Align.Applications >>> dir(Bio.Align.Applications) |
| − | >>> dir(Bio.Align.Applications) | + | ***from Bio.Emboss.Applications import NeedleCommandline |
*[http://www.broadinstitute.org/annotation/medea/stackmap/ Multi MEDIA] | *[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== | ||
| + | *[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] | ||
| + | **[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. | ||
| + | **Output = [http://genome.ucsc.edu/FAQ/FAQformat.html#format5 Multiple Alignment Format (MAF)] | ||
| + | <pre> | ||
| + | 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. | ||
| + | </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... | ||
| + | **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 | ||
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
- 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)
- 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
- compile library files...
