Bioinformatic software

Ebook "Protein modelling" detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction.

332p tudohanhtau1006 29-03-2024 2 1   Download

Ebook "Introduction to mathematical methods in bioinformatics" looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

305p tachieuhoa 28-01-2024 6 2   Download

Ebook "Java for bioinformatics and biomedical applications" represents an important development, giving the reader an opportunity to discover how the use of open and reusable Java code can solve large bioinformatics problems in a software engineered and robust way. This has lead to an explosion of interest in the subject, and a similar explosion in tools and data resources for researchers to learn and use in their work.

353p tachieuhoa 28-01-2024 8 5   Download

Ebook "Applied bioinformatics: An introduction" introduces readers to the basic principles of bioinformatics and the practical application and utilization of computational tools, without assuming any prior background in programming or informatics. It provides a coherent overview of the complex field and focuses on the implementation of online tools, genome databases and software that can benefit scientists and students in the life sciences.

297p tachieuhoa 28-01-2024 7 2   Download

Ebook "Theory and mathematical methods for bioinformatics" on biomathematics published within the past ten years have consisted of collections of standard bioinformatics problems and informational methods, and focus mainly on the logistics of implementing and making use of various websites, databases, software packages and serving platforms. While these types of books do introduce some mathematical and computational methods alongside the software packages, they are lacking in a systematic and professional treatment of the mathematics behind these methods.

450p tachieuhoa 28-01-2024 5 2   Download

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research.

9p visteverogers 24-06-2023 8 2   Download

Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. Results: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes.

10p viaristotle 29-01-2022 10 0   Download

Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns.

23p viarchimedes 26-01-2022 5 0   Download

Terminal differentiation-induced ncRNA (TINCR) plays an essential role in epidermal differentiation and is involved in the development of various cancers. The relationships among TINCR, miR-210, and BTG2 were investigated by bioinformatics software and luciferase reporter assay. The in vivo function of TINCR was accessed on survival rate and tumor growth in nude mice.

16p vimahuateng 26-11-2021 5 0   Download

Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results.

8p vitzuyu2711 29-09-2021 12 1   Download

Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi.

7p visilicon2711 20-08-2021 10 1   Download

DNA methylation is a major epigenetic modification involved in regulating gene expression. The effects of DNA methylation on gene expression differ by genomic location and vary across kingdoms, species and environmental conditions. To identify the functional regulatory roles of DNA methylation, the correlation between DNA methylation changes and alterations in gene expression is crucial.

10p vijeeni2711 24-07-2021 14 0   Download

The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (sub- )cellular populations.

11p vilichoo2711 23-06-2021 13 2   Download

MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species.

9p viwyoming2711 16-12-2020 6 1   Download

Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used.

13p viwyoming2711 16-12-2020 7 0   Download

An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process.

14p viwyoming2711 16-12-2020 20 1   Download

Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, fexible metadata collection and linkage of related experimental data generated locally by vendor software.

7p viwyoming2711 16-12-2020 9 0   Download

New technologies for analyzing biological samples, like next generation sequencing, are producing a growing amount of data together with quality scores. Moreover, software tools (e.g., for mapping sequence reads), calculating transcription factor binding probabilities, estimating epigenetic modification enriched regions or determining single nucleotide polymorphism increase this amount of position-specific DNA-related data even further.

9p vikentucky2711 26-11-2020 12 1   Download

SEUDOMARKER is a software package that performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-controls and pedigrees of varying structure into a single unified analysis.

8p vikentucky2711 26-11-2020 11 0   Download

Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform.

9p vikentucky2711 26-11-2020 18 0   Download