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Related Concept Videos

Sequences01:29

Sequences

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 the...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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...
Arithmetic Sequences01:30

Arithmetic Sequences

An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the term...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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 DNA...
Geometric Sequences01:30

Geometric Sequences

In systems where values diminish by a constant proportion at each stage, the resulting sequence follows a geometric structure. Each new value in the sequence is obtained by applying a fixed multiplier to the preceding term. This regular, proportional decline type is often used to represent processes involving gradual loss, such as energy dissipation or reduction in amplitude over time.When analyzing the total effect of such a process across unlimited iterations, the series of values is referred...
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...

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Related Experiment Video

Updated: Jun 7, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

NEFFy: a versatile tool for computing the number of effective sequences.

Maryam Haghani1, Debswapna Bhattacharya1, T M Murali1

  • 1Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States.

Bioinformatics (Oxford, England)
|June 3, 2025
PubMed
Summary

NEFFy is a new standalone tool for calculating the Number of Effective Sequences (NEFF) in multiple sequence alignments. It offers comprehensive options and supports proteins, RNAs, and DNAs for evolutionary analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Multiple Sequence Alignments (MSAs) contain crucial evolutionary data for predicting protein and nucleic acid structure and function.
  • The Number of Effective Sequences (NEFF) quantifies sequence diversity within an MSA.
  • Existing tools for NEFF calculation are not standalone and lack comprehensive options.

Purpose of the Study:

  • To develop the first standalone software package, NEFFy, for calculating NEFF.
  • To integrate all available NEFF calculation options.
  • To support diverse MSA formats and biological macromolecules (proteins, RNAs, DNAs).

Main Methods:

  • NEFFy was developed as open-source software with C++ source code and a Python wrapper.
  • The tool integrates all known NEFF calculation options.
  • It supports various MSA formats and is designed for proteins, RNAs, and DNAs.

Main Results:

  • NEFFy is the first software package to calculate NEFF across diverse MSA formats for proteins, RNAs, and DNAs.
  • It surpasses existing tools in functionality, computational efficiency, and scalability.
  • NEFFy provides per-residue NEFF calculation and supports MSAs of multimeric proteins.

Conclusions:

  • NEFFy offers a comprehensive, efficient, and scalable solution for NEFF calculation.
  • The tool enhances evolutionary analysis by providing detailed insights into MSA diversity.
  • NEFFy is readily available as open-source software with extensive documentation.