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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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lncRNA - Long Non-coding RNAs02:39

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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RNA-seq03:21

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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. 
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Related Experiment Video

Updated: Sep 5, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms.

Anna C Nelson Dittrich1, Andrew D L Nelson2

  • 1Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 11, 2022
PubMed
Summary

Evolinc-II is a new tool that automates comparative genomic analysis to find conserved long noncoding RNAs (lncRNAs). This pipeline helps researchers prioritize these important molecules for functional studies.

Keywords:
BioinformaticsComparative genomicsCyVerseDockerFunctional genomicsGenome annotationLong intergenic noncoding RNAsRNA evolutionRNA structure

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Long noncoding RNAs (lncRNAs) play crucial roles in gene regulation.
  • Identifying and functionally characterizing lncRNAs is challenging due to their diversity and complexity.
  • Comparative genomic and transcriptomic analyses are essential for prioritizing lncRNAs for functional studies.

Purpose of the Study:

  • To introduce Evolinc-II, a novel bioinformatic pipeline for automated comparative analysis of lncRNAs.
  • To enable the identification of sequence and structural conservation across thousands of lncRNAs simultaneously.
  • To facilitate the inference of evolutionary events in lncRNA emergence and prioritize them for functional analysis.

Main Methods:

  • Evolinc-II utilizes comparative genomic and transcriptomic approaches.
  • The pipeline performs automated searches for sequence and structural conservation.
  • A phylogenetic approach is employed to infer evolutionary events related to lncRNA emergence.

Main Results:

  • Evolinc-II automates the analysis of large numbers of lncRNAs.
  • The pipeline identifies conserved lncRNA homologs.
  • Evolinc-II aids in prioritizing lncRNAs for subsequent functional characterization.

Conclusions:

  • Evolinc-II provides an efficient and automated method for lncRNA comparative analysis.
  • The tool supports both command-line and graphical user interface (GUI) usage.
  • Evolinc-II is valuable for researchers aiming to understand lncRNA evolution and function.