Wikiomics:Genome aligners: Difference between revisions
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* MULAN | * MULAN | ||
* GeLo http://synteny.cnr.berkeley.edu/CoGe/GEvo.p | * GeLo http://synteny.cnr.berkeley.edu/CoGe/GEvo.p | ||
=Supporting tools= | |||
* DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes (Perl) | |||
http://dagchainer.sourceforge.net/ | |||
=Useful links= | |||
* how to create a synteny map between two genomes: http://synteny.cnr.berkeley.edu/wiki/index.php/SynMap | |||
Revision as of 10:04, 23 April 2010
List of programs used for large scale DNA alignment. At the moment the statements are mostly from web sites of programs in question.
For introduction read: Lyons and Freeling "How to usefully compare homologous plant genes and chromosomes as DNA sequences" 2008
Aligners
- LAGAN Toolkit
http://lagan.stanford.edu/lagan_web/index.shtml ver 2.0 from 2006
- LAGAN
- M-LAGAN
- Shuffle-LAGAN
- lastz (successor of blastz)
latest release: 2010-Jan-12 http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
- last
http://last.cbrc.jp/ last release: last-103.zip from 05-Apr-2010
Compare two vertebrate genomes (Human vs. mouse: 1 day on 1 CPU) copes more efficiently with repeat-rich sequences can align a large number of sequences (i.e. next gen sequencing data to genome)
- YASS
http://bioinfo.lifl.fr/yass/ last release: pre-release v1.14 build Apr 15, 2010 paper; doi:10.1093/nar/gki478
spliced seeds, see also links to hedera & iedera programs on YASS page.
- MAUVE (multiple genome alignment) http://asap.ahabs.wisc.edu/mauve/
last release: 2.3.1, from November 11th 2009. Java application with GUI. Simple to use, producing colorful graphic. Output gets too cluttered with too many / too divergent sequences.
- Spines (software collection from Broad) http://www.broadinstitute.org/science/programs/genome-biology/spines
latest release: spines-1.09.tar.gz from 2010-04-01
- Satsuma "highly parallelized program for high-sensitivity, genome-wide synteny"
- Papaya "an all-purpose alignment tool for less diverged sequences"
- SLAP "context-sensitive local aligner for diverged sequences with large gaps"
Alignment visualisation
- VISTA http://genome.lbl.gov/vista
- MULAN
- GeLo http://synteny.cnr.berkeley.edu/CoGe/GEvo.p
Supporting tools
- DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes (Perl)
http://dagchainer.sourceforge.net/
Useful links
- how to create a synteny map between two genomes: http://synteny.cnr.berkeley.edu/wiki/index.php/SynMap
