Related Experiment Video
Updated: Sep 17, 2025
10:20
In vitro Digestion of Emulsions in a Single Droplet via Multi Subphase Exchange of Simulated Gastrointestinal Fluids
Published on: November 18, 2022
2.7K
Fast and flexible minimizer digestion with digest.
Alan Zheng1, Ishmeal Lee1, Vikram S Shivakumar1
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, United States.
Bioinformatics (Oxford, England)
|June 28, 2025
Summary
A new open-source tool called Digest efficiently processes genomic sequences using minimizer, modimizer, or syncmer digestion. This bioinformatics tool is designed for scalability and speed in sequence analysis.
Area of Science:
- Bioinformatics and Computational Biology
- Genomic Data Analysis
- Sequence Analysis
Background:
- Minimizer digestion is a key technique in bioinformatics tools.
- Applications include de Bruijn graph assembly and sequence classification.
- Efficient sequence processing is crucial for large genomic datasets.
Purpose of the Study:
- To introduce a new open-source tool and library for efficient genomic sequence digestion.
- To provide a flexible tool supporting minimizers, modimizers, and syncmers.
- To enhance the performance of bioinformatics pipelines.
Main Methods:
- Developed an open-source tool named Digest.
- Implemented in C++17 with a Python API and Rust bindings.
- Utilizes efficient data structures for scalable multi-threaded processing.
Main Results:
- Digest facilitates efficient digestion of genomic sequences.
- The tool supports minimizers, modimizers, and syncmers.
- Achieves expected spacings between digested elements and scales well with threads.
Conclusions:
- Digest is a valuable open-source resource for bioinformatics.
- It offers efficient and scalable sequence digestion capabilities.
- The tool supports various digestion strategies for diverse applications.
More Related Videos
Related Concept Videos
01:02Protein Digestion
106.0K
Protein digestion begins in the stomach, where the highly acidic environment can easily disrupt protein structure by exposing the peptide bonds of polypeptide chains. After polypeptide chains are broken into individual amino acids by a series of digestive enzymes, the amino acids are transported to the liver via the bloodstream to produce energy.
106.0K
01:30Mechanical and Chemical Digestion in the Small Intestine
1.5K
The small intestine plays a crucial role in our digestive system, performing both mechanical and chemical digestion.
Mechanical digestion in the small intestine involves movements such as segmentations and migrating motility complexes (MMCs), primarily controlled by the myenteric plexus. Segmentations are localized contractions occurring in areas of the intestine distended by chyme—a mixture of partially digested food. These contractions mix chyme with digestive juices, facilitating...
Mechanical digestion in the small intestine involves movements such as segmentations and migrating motility complexes (MMCs), primarily controlled by the myenteric plexus. Segmentations are localized contractions occurring in areas of the intestine distended by chyme—a mixture of partially digested food. These contractions mix chyme with digestive juices, facilitating...
1.5K
01:06Lipid Digestion
94.1K
Lipids are large molecules that are generally not water-soluble. Since most of the digestive enzymes in the human body are water-based, there are specific steps the body must take to break down lipids and make them available for use.
94.1K
01:50What is Monogastric Digestion?
72.6K
The human body contains a monogastric digestive system. In a monogastric digestive system, the stomach only contains one chamber in which it digests food. Several other animal species also have monogastric digestive systems, including pigs, horses, dogs, and birds. This chapter, however, focuses on the human digestive system.
72.6K
01:22Physiology of the Gastrointestinal System II: Digestion and Absorption
984
The gastrointestinal (GI) tract, extending from the mouth to the anus, plays a pivotal role in the digestion and absorption of nutrients. This process involves both mechanical and chemical actions facilitated by various enzymes.
Digestion begins in the mouth, where food undergoes mechanical breakdown by chewing and combines with saliva. Salivary amylase, an enzyme in saliva, starts the breakdown of starches into maltose. The food then travels down the esophagus to the stomach.
In the stomach, a...
Digestion begins in the mouth, where food undergoes mechanical breakdown by chewing and combines with saliva. Salivary amylase, an enzyme in saliva, starts the breakdown of starches into maltose. The food then travels down the esophagus to the stomach.
In the stomach, a...
984
01:29Intestinal Phase of Digestion
5.5K
The intestinal phase of digestion is the third and final stage of the digestive process, occurring after the cephalic and gastric phases. It begins when chyme, a partially digested mixture of food and digestive enzymes, enters the small intestine from the stomach. This phase is crucial for nutrient absorption and involves complex hormonal and enzymatic interactions.
The arrival of the chyme in the small intestine distends the duodenum, which triggers the enterogastric reflex. This distension...
The arrival of the chyme in the small intestine distends the duodenum, which triggers the enterogastric reflex. This distension...
5.5K