In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, bot...

To determine whether unchlorinated bore water in northern Australia contained Burkholderia pseudomallei organisms, we sampled 55 bores; 18 (33%) were culture positive. Multilocus sequence typing identified 15 sequence types. The B. pseudomallei sequence type from 1 water sample matched a clinical isolate from a resident with melioidosis on the same property.

Aerosol chemical and optical properties over the Paris area within ESQUIF project A. Hodzic, R. Vautard, P. Chazette, L. Menut, and B. Bessagnet Laboratoire de Météorologie Dynamique, Institut Pierre-Simon Laplace, Palaiseau, France Laboratoire des Sciences du Climat et de l’Environnement, Institut Pierre-Simon Laplace, Gif sur Yvette, France Institut National de l’Environnement Industriel et d...

Citation: Yang X, Yu S, Wu Q, Zhang J, Wu S and Rong D (2018) Multilocus Sequence Typing and Virulence-Associated Gene Profile Analysis of Staphylococcus aureus Isolates From Retail Ready-to-Eat Food in China. Front. Microbiol. 9:197. doi: 10.3389/fmicb.2018.00197 Multilocus Sequence Typing and Virulence-Associated Gene Profile Analysis of Staphylococcus aureus Isolates From Retail Ready-to-Eat...

We present a method whose purpose is to post-process the fuzzy results of secondary structure prediction methods that use multiple sequence alignments, in order to obtain 'realistic' secondary structures, i.e., secondary structure elements whose length is greater than or equal to some predefined minimum length. This regularization helps with interpretation of the secondary structure prediction.

Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in different species. In a recent study, the influence of heterotachy on the per...

The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignm...

A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins.

Subjects made delayed pitch comparisons when the standard and comparison tones were separated by a sequence of interpolated tones. In some conditions, a tone of the same pitch as the standard tone was included among the interpolated tones. Recognition performance was superior for sequences where the standard tone pitch was repeated, even compared with control sequences of reduced size. The impr...

The distribution of optimal local alignment scores of random sequences plays a vital role in evaluating the statistical significance of sequence alignments. These scores can be well described by an extreme-value distribution. The distribution's parameters depend upon the scoring system employed and the random letter frequencies; in general they cannot be derived analytically, but must be estima...