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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
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...
Retroviruses02:33

Retroviruses

Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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 13, 2026

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

CoRSeqV3-C: a novel HIV-1 subtype C specific V3 sequence based coreceptor usage prediction algorithm.

Kieran Cashin1, Lachlan R Gray, Martin R Jakobsen

  • 1Center for Virology, Burnet Institute, 85 Commercial Rd, Melbourne 3004VIC, Australia.

Retrovirology
|March 1, 2013
PubMed
Summary
This summary is machine-generated.

A new algorithm, CoRSeqV3-C, accurately predicts HIV-1 subtype C coreceptor usage. This tool helps clinicians choose optimal treatments for HIV-1 subtype C infections.

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Last Updated: May 13, 2026

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
19:57

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Published on: March 30, 2014

Area of Science:

  • Virology
  • Immunology
  • Computational Biology

Background:

  • HIV-1 subtype C (C-HIV) is the predominant strain globally, increasingly found in developed nations.
  • Accurate determination of C-HIV coreceptor usage is vital for effective treatment selection, including CCR5 antagonist maraviroc (MVC).
  • In silico prediction algorithms offer a rapid and cost-effective method for assessing HIV-1 coreceptor tropism.

Purpose of the Study:

  • To elucidate the V3 sequence determinants of C-HIV coreceptor usage.
  • To develop and validate a novel, sensitive, and user-friendly C-HIV specific coreceptor usage prediction algorithm.

Main Methods:

  • Characterization of phenotypically-verified C-HIV gp120 V3 sequences from the Los Alamos HIV Database.
  • Comparative sequence analyses of R5 and CXCR4-using C-HIV V3 sequences.
  • Development and validation of the CoRSeqV3-C prediction algorithm.

Main Results:

  • CXCR4-using C-HIV V3 sequences exhibit greater amino acid variability, net charge, and length compared to R5 C-HIV V3 sequences.
  • Significant differences were observed in the GPGQ crown motif and glycosylation sites between CXCR4-using and R5 C-HIV strains.
  • The developed CoRSeqV3-C algorithm demonstrated superior sensitivity in predicting CXCR4 usage for C-HIV strains compared to existing algorithms.

Conclusions:

  • CoRSeqV3-C is a highly sensitive V3 sequence-based algorithm for predicting CXCR4 usage in C-HIV strains, maintaining specificity.
  • The algorithm is openly available for public use.
  • CoRSeqV3-C can aid clinicians in selecting appropriate treatments for C-HIV infections and support pathogenesis research.