In our method, we utilize a set of d chains to sample inversion paths in parallel.
If the sampled inversion is indeed a sorting inversion (decided by Bader's algorithm in linear time), the change is accepted with the probability in equation (8).
Five serum pools were created (TB group; control group; three other microbial infection groups (BP, VZV and EV) by combining 20 samples (20 μl per sample) and mixing by inversion and 400 μl of each of these pools was used to extract RNA for assay by TaqMan Low-Density Array (TLDA).
5 ml of a 10 mg/ml solution of proteinase K (BMB) was added and the sample was mixed by inversion and incubated at 55°C for 60 min. The sample was extracted with an equal volume of TE saturated phenol and again with PCI (TE saturated phenol, chloroform, isoamyl alcohol, 25:25:1).
Each sample was mixed by inversion and allowed to precipitate at -20°C for one hour.
Briefly, samples were mixed by inversion, and then incubated overnight at 50°C.
The samples were mixed by inversion and incubated at 98°C for 10 minutes.
Samples were centrifuged 5 minutes 20,817 rpm at 4°C, the upper layer was transferred to a new microfuge tube containing 500 μL EtOH (500 μl), the samples were mixed by inversion, and the RNA purification was performed using the RNeasy kit (Qiagen) according to manufacturer's instructions, and the RNA was eluted in 90 μl of RNase-free water.
Ice-cold absolute ethanol : sodium acetate (25 : 1; 600 µL) was added gently and mixed by inversion, and a sample incubated at −20 °C for 45 min. DNA was pelleted by centrifugation at 4000 rpm for 20 min. The supernatant was removed; the pellet was washed with 500 µL of 70%% ethanol and left to stand for 5 min, then washed twice.
Bayesian methods have also been developed to sample histories of inversions and transposition (Miklos, 2003), duplications (Zhang, 2008), gene gain and loss and gene conversion and nucleotide substitution (Didelot and Falush, 2007).
