Related Concept Videos
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
Gordon Gremme1, Sascha Steinbiss, Stefan Kurtz
1University of Hamburg, Hamburg.
Summary
GenomeTools provides a unified graph-based representation for efficient genome annotation processing. This software library handles large datasets with low memory overhead, enabling streamlined bioinformatics workflows.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Genome annotations are commonly stored in plain text files, relying on implicit annotation graphs.
- Managing and processing complex genomic feature data presents computational challenges.
Purpose of the Study:
- To introduce GenomeTools, a software library and tools for creating, processing, and converting genome annotation graphs.
- To offer a unified, graph-based representation for intuitive access and manipulation of genomic features.
Main Methods:
- Developed an object-oriented, C-based software library adhering to the annotation graph approach.
- Implemented an efficient pull-based approach for sequential processing of annotations to minimize memory usage.
- Designed for seamless integration into bioinformatics workflows, with support for compressed sequence data access.
Main Results:
- GenomeTools provides a unified graph-based representation for genomic features.
- The pull-based processing enables efficient handling of large annotation sets, including human variation data.
- The C implementation ensures a lightweight memory footprint and facilitates language bindings (e.g., Python, Ruby).
Conclusions:
- GenomeTools offers a powerful and efficient solution for genome annotation management and processing.
- The library simplifies the development of bioinformatics software by providing intuitive access to annotation data.
- Its design supports scalability and interoperability with various programming languages.