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)

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-1.11.tar.gz from 2010-10-28

• 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"

Mercator

Multiple Whole-Genome Orthology Map Construction

http://www.biostat.wisc.edu/~cdewey/mercator/

latest release: cndsrc-2010.10.11.tar.gz

Enredo-Pecan-Ortheus pipeline

Several programs used for aligning eukariotic genomes at ENSEMBL.

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