What is the meaning of scaffold in genomics?
Best insight from top research papers
In genomics, scaffolding refers to the process of ordering and orienting contigs (pre-assembled DNA sequences) to create longer and more continuous sequences, ultimately aiding in the assembly of a draft genome . This step is crucial for obtaining a more complete and accurate reference genome, which serves as a foundation for various genomic analyses and downstream applications . Scaffolding methods utilize various types of sequencing data, such as alignments between contigs and reads, to determine the relative positions and orientations of contigs, resulting in extended scaffolds that enhance the quality of genome assembly . Additionally, advancements in high-throughput sequencing technologies have led to the development of diverse scaffolding methods, including reference-based scaffolding and multiple reference-based scaffolding, to address challenges posed by genome complexity and evolutionary relationships .
Answers from top 5 papers
More filters
| Papers (5) | Insight |
|---|---|
21 Aug 2020 | In genomics, scaffolding refers to ordering and orienting contigs in a draft genome to create larger scaffolds, aiding in genome assembly for a more complete sequence. |
| In genomics, a scaffold is a framework where pre-assembled genomic regions are arranged using linking information, aiding in genome sequencing and assembly. | |
| Scaffolding in genomics refers to determining the relative position and orientation of contigs to complete the assembly process, treated as a paths and cycles cover problem on a scaffold graph. | |
9 Citations | Scaffolds in genomics refer to ordered and oriented sets of contigs, aiding in assembling a more complete and contiguous reference genome, crucial for genomic research and downstream analysis. |
| Scaffolding in genomics refers to ordering and orienting contigs in a draft genome based on a reference genome, aiding in genome rearrangement for accurate sequencing. |
Related Questions
How size of pores in scaffolds affects cultivated cells?5 answersThe size of pores in scaffolds significantly influences cultivated cells in tissue engineering. Larger pore sizes, such as those exceeding 100 μm, promote cellular infiltration and enhance osteogenic properties. Different cell types exhibit varying preferences for scaffold pore sizes, affecting adhesion, proliferation, and differentiation rates. For instance, human umbilical vein endothelial cells (HUVECs) and bone marrow mesenchymal stem cells (BMSCs) demonstrate good angiogenic responses and osteogenic differentiation on scaffolds with larger pores. Techniques to enlarge pore sizes in electrospun scaffolds have been explored to optimize cell behavior, including adhesion, proliferation, and infiltration. Geometrical control of micronetwork structures formed by endothelial cells is influenced by scaffold pore sizes, impacting network density and formation. In conclusion, scaffold pore size plays a crucial role in modulating cell behavior and tissue regeneration outcomes.
Design of scaffolding in cardiac tissue engineering?4 answersThe design of scaffolding in cardiac tissue engineering is a crucial aspect of creating functional cardiac constructs. Various approaches have been explored in the literature. Ketabat et al. developed cardiac constructs using a novel angular structure mimicking cardiac architecture from alginate and gelatin composite, which showed promising properties for cardiac tissue engineering. Schmitt et al. introduced a customizable scaffold composed of wet-spun polycaprolactone (PCL) microfibers to strengthen engineered tissues and provide an anisotropic mechanical environment. Rioux et al. presented a technique for rapid fabrication of native-like tricuspid aortic valve scaffolds made of an alginate-based hydrogel, which accurately reproduced the complex three-dimensional anatomy of the aortic valve. English et al. explored micropatterning the surfaces of fibrin gels to mimic anisotropic native tissue architecture and promote cellular alignment of human induced pluripotent stem cell cardiomyocytes (hiPS-CM). Ruocco et al. engineered a biomimetic in vitro model using polycaprolactone (PCL)-based scaffolds with randomly oriented fibers, surface-functionalized with human type I collagen and fibronectin, to mimic fibrotic cardiac tissue-like ECM composition.
What is scaffolding?4 answersScaffolding is a multi-step process in which student assignments support and progressively build on one another, culminating in the completion of a larger project. It involves students choosing topics of interest and completing assignments that build on one another, while receiving ongoing feedback from the instructor. This approach helps students improve their writing skills while exploring new content. Scaffolding is the support provided to students by the learning environment, including the teacher, curricular design, technological tools, and classroom social practices. It simplifies tasks, supports learners in participating in authentic disciplinary practices, and helps them focus on the most important aspects of the problem. Effective scaffolding is adaptable and contingent on the learner's evolving understanding, gradually reducing structure as the learner progresses. It can be inferred using digital traces or dynamic software.
What is a genome?5 answersA genome is the complete set of genetic material in an organism, including all the genes and non-coding DNA sequences. It represents the blueprint for an organism's traits and is passed down from generation to generation. The concept of a genome has evolved over time, from a structural interpretation of the haploid number of chromosomes to encompassing all the material in the nucleus and the sum of nucleotide base sequences. The genome is not only a repository of information but also plays a role in the regulation of cell physiology and the diversity of an organism. Advances in genomics research have led to the deciphering of the genomes of various organisms, providing insights into their biology and potential applications in medicine. Understanding the genome is crucial for studying evolution, gene function, and developing personalized therapies based on an individual's genetic makeup.
What is scaffold?5 answersA scaffold is a structure used in construction to provide a safe working area and support for workers. It can be used for various purposes such as bridging steel beams, constructing large-sized wall parts for building external walls, and providing a platform for workers to stand on. Scaffolds can be made of different materials, including steel and polymeric components. They are designed to ensure construction safety, provide a good construction space, and allow for rapid and simple detachment during aloft work. Scaffolds can also be used in tissue engineering for wound healing and tissue regeneration. They are used as carriers for cell and drug delivery, promoting the differentiation of cells and production of growth factors to enhance wound healing. Overall, scaffolds play a crucial role in construction and tissue engineering, providing support, safety, and facilitating various construction and healing processes.
Have scaffolds been used for non-viral gene delivery to target scar cells in spinal cord injury?5 answersScaffolds have been used for non-viral gene delivery to target scar cells in spinal cord injury. Biomaterial scaffolds combined with stem cell therapy or other regenerative therapy can facilitate cell-material interactions and neuroprotection. A 3D fiber-hydrogel scaffold consisting of aligned electrospun fibers and collagen matrix has been developed for sustained delivery of microRNAs (miRs) to enhance axon regeneration. Injectable hyaluronic acid (HA) scaffolds with macropores have been shown to increase the expression of locally delivered transgenes and promote cell and axon infiltration into the scaffolds. Additionally, a three-dimensional aligned nanofibers-hydrogel scaffold has been used for sustained non-viral delivery of proteins and small non-coding RNAs to promote axon regeneration and prevent scar tissue formation.