Category:Genome-Comparison Software

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A number of tools have been created for use in the field of comparative genomics. This page attempts to capture broad-level information associated with each tool. Feel free to edit this table as you see fit.

Comparison of Available Software

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Name Global/Local Pairwise/Multiple Desc/Notes Open Source URL Reference(s)

MUMmer

Global

Pairwise

  • comes with other programs and an alignment viewer (v3.0)

Yes, as of version 3.0

http://mummer.sourceforge.net/

PMID:14759262[1]

Mauve

glocal - uses local alignments to guide a global alignment

Multiple

  • uses an anchor-based-approach, MUMs
  • handles large-scale evolutionary changes well (rearrangements, horizontal transfer, insertions/deletions, etc.)

No, freely distributed.

http://asap.ahabs.wisc.edu/mauve/

PMID:15231754[2]

MGA - Multiple Genome Aligner

Glocal

Multiple

  • extends the idea of MUMs to multiple genomes
  • works best with closely related sequences (doesn't take rearrangements into consideration)

No, freely available

http://bibiserv.techfak.uni-bielefeld.de/mga/

PMID:12169561[3]

GAME

Local

Pairwise

  • an anchor filtering scheme
  • incorporates the translation into the filtering scheme to increase sensitivity
  • adjustable parameters for filtering allow comparison across different phylogenetic distances

http://platcom.informatics.indiana.edu/game

PMID:15979044[4]

EMAGEN -
Efficient Multiple Alignment algorithm for whole GENomes

Glocal

Multiple

http://portal.acm.org/citation.cfm?id=976536

edit table

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Other Resources

  • Field et al. 2005 describes a number of databases and software used in comparative genomics

References

  1. ↑ Kurtz, S et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5 R12 PubMed
  2. ↑ Darling, AC et al. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14 1394-403 PubMed
  3. ↑ Höhl, M et al. (2002) Efficient multiple genome alignment. Bioinformatics 18 Suppl 1 S312-20 PubMed
  4. ↑ Choi, JH et al. (2005) GAME: a simple and efficient whole genome alignment method using maximal exact match filtering. Comput Biol Chem 29 244-53 PubMed

Pages in category "Genome-Comparison Software"

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