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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

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.

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Related Experiment Video

Updated: May 23, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

A new algorithm for quantifying binding site pattern similarity with applications for Next Generation Sequencing.

Paul W Bible1, Rasiah Loganantharaj

  • 1University of Louisiana, Lafayette, LA 70503, USA. pwb4552@louisana.edu

International Journal of Bioinformatics Research and Applications
|March 28, 2012
PubMed
Summary
This summary is machine-generated.

We developed PfmSim, a new algorithm for comparing transcription factor binding patterns represented as Position Frequency Matrices (PFMs). PfmSim improves the accuracy of similarity detection and classification of regulatory sequences.

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Last Updated: May 23, 2026

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Transcription factor ChIP-seq experiments provide regulatory data.
  • Motif analysis of this data offers insights into biological function.
  • Position Frequency Matrices (PFMs) represent transcription factor binding patterns.

Purpose of the Study:

  • To develop a novel algorithm for gapped alignment of PFMs.
  • To compare the developed algorithm with existing measures for similarity and classification tasks.

Main Methods:

  • Developed a novel gapped alignment algorithm for PFMs, named PfmSim.
  • Compared PfmSim against the Sandelin and Wasserman standard measure.
  • Evaluated performance on similarity and classification tasks.

Main Results:

  • PfmSim provides improved similarity values compared to the standard measure.
  • The algorithm demonstrates enhanced performance in classification tasks.

Conclusions:

  • PfmSim offers a more accurate method for comparing transcription factor binding patterns.
  • This advancement facilitates more sophisticated detection and classification of regulatory sequences.