Wikiomics:Genome aligners

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

• Vmatch

http://www.vmatch.de/

• 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
• MULAN
• GeLo
• Gmaj

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