Related Experiment Video
Updated: Apr 23, 2026

09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.1K
ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.
1ProfileGrid.org, P.O. Box 6414, Irvine, California 92616, USA.
BMC Proceedings
|September 20, 2014
Summary
ProfileGrids offer a novel visualization for large protein multiple sequence alignments, improving upon Sequence Logos. JProfileGrid software enables effective analysis of conservation and diversity patterns in protein families.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Evaluating visualization paradigms for large protein multiple sequence alignments.
- Limitations of Sequence Logos for protein alignment visualization.
- Introduction of ProfileGrids as an alternative visualization method.
Purpose of the Study:
- To assess the effectiveness of ProfileGrids for visualizing protein multiple sequence alignments.
- To compare ProfileGrids with existing Sequence Logo representations.
- To introduce and utilize the JProfileGrid software for this analysis.
Main Methods:
- Utilized the JProfileGrid software to analyze protein multiple sequence alignment datasets from the 2013 BioVis Contest.
- Generated visualizations using the ProfileGrid paradigm.
- Compared ProfileGrid outputs with Sequence Logo reference images.
Main Results:
- ProfileGrids provide a clear and effective representation of protein multiple sequence alignments.
- The visualization facilitates analysis of conservation and diversity patterns.
- Interactive querying of residue distributions within the alignment is supported.
Conclusions:
- ProfileGrid representation is a powerful tool for analyzing protein multiple sequence alignments.
- JProfileGrid software offers a free and accessible solution for implementing this visualization.
- This method enhances understanding of sequence conservation and variation in protein families.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
5.8K
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...
5.8K
Next-generation Sequencing
87.4K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.4K
Maxam-Gilbert Sequencing
10.3K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
10.3K
Sanger Sequencing
800.2K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
800.2K
Sequence Networks of Rotating Machines
590
A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
590
Sequences
491
Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
491

