Related Experiment Video
Updated: Mar 3, 2026
08:48
Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays
Published on: November 29, 2014
14.5K
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences
Xuebing Wu1,2, David P Bartel1,2
1Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Nucleic Acids Research
|May 2, 2017
Summary
New tool kpLogo detects ultra-short, position-specific motifs missed by other methods. This probability-based sequence analysis tool aids in understanding key molecular interactions.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- Short sequence motifs (1-4 letters) are crucial in macromolecules.
- Existing motif discovery tools often fail to identify position-specific ultra-short motifs.
Purpose of the Study:
- To develop a novel tool, kpLogo, for detecting and visualizing position-specific ultra-short motifs.
- To overcome limitations of conventional motif visualization tools in handling positional dependencies and weighted sequences.
Main Methods:
- Developed kpLogo, a probability-based logo tool.
- Integrated detection and visualization of position-specific motifs from aligned sequences.
- Addressed limitations in handling positional interdependencies and ranked/weighted sequences.
Main Results:
- kpLogo successfully detects and visualizes position-specific ultra-short motifs.
- The tool handles positional interdependencies effectively.
- kpLogo utilizes ranked or weighted sequences from high-throughput assays.
Conclusions:
- kpLogo provides an effective solution for identifying critical ultra-short motifs.
- The tool enhances motif discovery and visualization in bioinformatics.
- kpLogo is available at http://kplogo.wi.mit.edu/
More Related Videos
Related Concept Videos
02:51Multi-species Conserved Sequences
4.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.9K
02:54Evolutionary Relationships through Genome Comparisons
7.1K
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...
7.1K
01:49Conserved Binding Sites
5.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.2K
01:29Modern Molecular Taxonomy
781
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
781
02:32Position-effect Variegation
7.2K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
7.2K