Related Experiment Video
Updated: Jun 1, 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
2.4K
Fast and flexible minimizer digestion with digest.
Alan Zheng1, Ishmeal Lee1, Vikram S Shivakumar1
1Department of Computer Science, Johns Hopkins University, 3400 N Charles St, 21218, Maryland, USA.
Biorxiv : the Preprint Server for Biology
|January 20, 2025
Summary
This study introduces Digest, a new open-source bioinformatics tool for efficient genomic sequence digestion using minimizers, modimizers, or syncmers. It offers scalable performance and controlled spacing for various bioinformatics applications.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Minimizer digestion is crucial for bioinformatics tools like De Bruijn-Graph assembly and sequence classification.
- Existing tools may lack efficiency or flexibility in genomic sequence digestion.
Purpose of the Study:
- To introduce a novel open-source tool and library for efficient genomic sequence digestion.
- To provide a flexible digestion method supporting minimizers, modimizers, and syncmers.
Main Methods:
- Developed an open-source tool named Digest using C++17 with a Python API.
- Implemented efficient data structures for scalable, multi-threaded processing.
- Enabled production of digests with controlled spacing between elements.
Main Results:
- Digest facilitates efficient digestion of genomic sequences.
- The tool demonstrates good scalability across multiple threads.
- Digests can be generated with expected spacings, enhancing usability.
Conclusions:
- Digest offers an efficient and flexible solution for genomic sequence digestion in bioinformatics.
- The open-source nature and Python API promote wider adoption and integration.
- This tool supports advanced sequence analysis tasks requiring precise genomic digests.
More Related Videos
Related Concept Videos
01:30Mechanical and Chemical Digestion in the Small Intestine
725
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...
725
01:50What is Monogastric Digestion?
70.5K
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.
70.5K
01:06Lipid Digestion
90.6K
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.
90.6K
01:02Protein Digestion
102.5K
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.
102.5K
01:29Intestinal Phase of Digestion
5.0K
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...
5.0K
00:57Carbohydrate Digestion
113.7K
Carbohydrate digestion and metabolism break down simple and complex carbohydrates from food into saccharides (i.e., sugars) for the body to use as energy. Carbohydrate digestion starts in the mouth during mastication, or chewing. The masticated carbohydrates remain intact in the stomach. Digestion resumes in the duodenum of the small intestine, where pancreatic alpha-amylase and brush border enzymes of the microvilli convert complex carbohydrates to monosaccharides. Finally, the monosaccharides...
113.7K