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Simulating Genome Evolution, Made Easier

Jonathan Eisen likes a paper on new software for simulating genome evolution. The paper, published in Genome Biology, comes out of Ian Holmes' lab at Berkeley. His team has written three new open-source programs that address inherent problems in current programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features), and SIMGENOME (for syntenic genome blocks). "Each offers algorithms for parameter measurement and reconstruction of ancestral sequence," says the abstract, and all three perform better than the leading neutral DNA simulator (DAWG) in benchmarks. You can download the programs at BioWiki.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.