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
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)
Use softmasked input sequences.
#create database from one of the genomes (larger?) on a machine with > 20GB free RAM to speed up the process lastdb -c -s20G -v genome1_db genome1_sequence.fa #align the genomes with maf output lastal -o genome2_vs_genome1.maf -v genome1_db genome2_sequence.fa
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.
Cgaln
http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/cgaln/ last release: Cgaln-1.0.0.tar.gz
Two step aligner (first at the blocks then nucleotide levels). According to authors, fast and memory efficient.
FEAST
http://monod.uwaterloo.ca/feast/ last release: feast-105-bin.tar.gz
more sensitive but slower than lastz, new tool not widely tested.
- 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
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
