Last year, we reported on SiBELia from Algorithmic Biology Lab in St. Petersburg.
Today is the first release of SiBELia Synteny Block ExpLoration tool! It ?nds synteny blocks in genomes represented as nucleotide sequences using approach based on de Bruijn graphs.
Son Pham, the senior of the research project, informed us that their paper is available from arxiv and got published in WABI 2013.
[Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes
Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham
Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we present Sibelia, a tool for finding synteny blocks in multiple closely related microbial genomes using iterative de Bruijn graphs. Unlike most other tools, Sibelia can find synteny blocks that are repeated within genomes as well as blocks shared by multiple genomes. It represents synteny blocks in a hierarchy structure with multiple layers, each of which representing a different granularity level. Sibelia has been designed to work efficiently with a large number of microbial genomes; it finds synteny blocks in 31 S. aureus genomes within 31 minutes and in 59 E.coli genomes within 107 minutes on a standard desktop. Sibelia software is distributed under the GNU GPL v2 license and is available at: this https URL Sibelia’s web-server is available at: this http URL.
Although Son Pham is in UCSD, he has been a long-term collaborator of Pavel Pevzner and that is the connection to St. Petersburg (if you are wondering).