Sibelia

Sibelia
(aka Synteny Block ExpLoration tool)

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. 

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

In version 2, Sibelia works with multiple strains of bacteria and partitions their genomes into synteny blocks — blocks of highly conserved regions among all compared genomes. It represents genomes in circos pictures [for publication] or interactive forms [for experts’ analysis].

Sibelia is under active development. If you see that Sibelia has a potential to support your research, please do not hesitate to contact us at vyahhi@bioinf.spbau.ru with a list of features you would like Sibelia to have.

Links:

• Download source code or binaries (Linux, Mac OS X and Windows).
• README, USAGE and INSTALL.
• Sibelia @ SEQWiki.
• Interactive examples.
• Please post bugs and issues here.

Related publications:

Ilya Minkin, Nikolay Vyahhi, Son Pham. "SyntenyFinder: A Synteny Blocks Generation and Genome Comparison Tool" (WABI 2012 poster)

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham. Sibelia: A fast synteny blocks generation tool for many closely related microbial genomes (submitted)

Acknowledgements

This work was supported by the Government of the Russian Federation (grant 11.G34.31.0018) and by the National Institutes of Health, USA (NIH grant 3P41RR024851-02S1).

Circos visualization:

The figure illustrates the hierarchy structure of synteny blocks between two strains of Helicobacter pylori: F32 and Gambia94/24.
Staphylococcus aureus subsp. aureus, strains JH1, N315, TW20 and MSSA476. Minimum size of a block = 10 000 bp.	Pseudomonas aeruginosa, strains UCBPP-PA14, PAO1 and NCGM2.S1. Minimum size of a block = 10 000 bp.	Helicobacter pylori, strains F32 and Gambia94/24. Minimum size of a block = 5000 bp.