Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as ß-defensin 4 (DEFB4) and its paralog HSPDP3.

Ultracold atom-atom collisions in a nonresonant laser field.

Using a recently developed approach for treating the three-dimensional anisotropic scattering we find considerable influence of a nonresonant laser field with intensity I> or =10(5) W/cm(2) on the Cs-Cs ultracold collisions. Strong dependence on the laser wavelength lambda(L) is shown at the optical region as lambda(L) becomes shorter than the critical value lambda(0) approximately 3000 nm (of the atomic de Broglie wave lambda) defining the region lambda(0)< or =lambda of the s-wave domination in the absence of the external field. Dependence on the laser polarization is also essential. The found effect can be applicable for controlling atom-atom interactions at ultralow temperatures.

Induced long-range dipole-field-enhanced antihydrogen formation in the p + Ps(n = 2) --> e(-) + H(n < or = 2) reaction.

We report high-precision calculations that correctly include the rearrangement channels by solving the modified Faddeev equations for energies between the Ps(n = 2) and H(n = 3) thresholds, which involve six and eight open channels. We find that 99% of the antihydrogen is formed in H(n = 2). Just above the Ps(n = 2) threshold the S, P, and D partial waves contribute nearly 1400pi(a(2)0) near the maximum. We find evidence that the induced long-range dipole potential is responsible for such a large H formation cross section. The possibility of utilizing this resonance to synthesize low-energy H is discussed.