Image co-registration requires special software, which is usually available for Unix workstations. This work presents two programs running under MS Windows, one for study co-registration and one for template creation. The co-registration can be done by minimising/maximising the count difference, squared difference, shape and mutual information. The quality of the fit can be estimated by evaluating the contours with different tools. The aligned images can be used for template creation. Both programs can be downloaded from http://www.homolka.cz/nm.

• Publikační typ
• časopisecké články MeSH

Food is characterized as one of the basic factors of the living environment of the human population and human health as the highest criterium of quality of these factors. Attention is paid above all to genotoxic agents in food in particular to mutagens and carcinogens which are formed during thermal treatment. The author makes the Czechoslovak professional public familiar with the pilot study of Hatch et al. of 1988 (13) which provides a list of 1007 references from the world literature on the possible genotoxicity of thermally treated food. The list is open and can be supplemented in the Lawrence National Laboratory in Livermore (USA) where it is at the same time available to everybody interested. Information is provided in "libget" software/rdb data base for the electronic computer system Unix. It is, however, also possible to obtain data from IBM PC(5.25") diskettes.

• MeSH
• analýza potravin * MeSH
• informační systémy MeSH
• mutageny analýza   MeSH
• vaření * MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• Názvy látek
• mutageny MeSH

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

• Publikační typ
• časopisecké články MeSH

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.

• Klíčová slova
• genome reconstruction, metagenome-assembled genomes, metagenomics, multi-domain, uncultivated viral genomes,
• MeSH
• Bacteria genetika   MeSH
• fylogeneze MeSH
• metagenom * MeSH
• metagenomika MeSH
• software MeSH
• viry * genetika   MeSH
• Publikační typ
• časopisecké články MeSH

DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller*.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the *.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).

• MeSH
• DNA chemie   genetika   MeSH
• hodnotící studie jako téma MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely * MeSH
• molekulární struktura MeSH
• software * MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH