MGRA web server

Developed by Computational Biology Lab


MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

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  1. M. A. Alekseyev and P. A. Pevzner. "Breakpoint Graphs and Ancestral Genome Reconstructions". Genome Research, 19 (5) (2009), pp. 943-957. doi:10.1101/gr.082784.108
  2. S. Jiang and M. A. Alekseyev. "Linearization of Median Genomes under DCJ". Proceedings of the 14th Workshop on Algorithms in Bioinformatics (WABI 2014), Lecture Notes in Computer Science 8701 (2014), pp. 97-106. doi:10.1007/978-3-662-44753-6_8
  3. P. Avdeyev, S. Jiang, S. Aganezov, F. Hu, and M. A. Alekseyev. "Reconstruction of ancestral genomes in presence of gene gain and loss", Journal of Computational Biology, 23 (3) (2016), pp.1-15. doi:10.1089/cmb.2015.0160 (bioRxiv doi:10.1101/040196)

Funding

The project is supported by the National Science Foundation under Grant No. IIS-1462107.