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Multi-species Conserved Sequences

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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.
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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...

Cis-regulatory Sequences

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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...

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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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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Testing the coding potential of conserved short genomic sequences.

¹Department of Statistics, Carnegie Mellon University, PA 15213, USA.

Advances in Bioinformatics

|March 13, 2010

Summary

This summary is machine-generated.

A new procedure identifies coding DNA in short genomic sequences by relaxing gene structure assumptions. This method enhances genomic databases with novel coding potential regions, improving gene discovery.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Identifying coding DNA within genomes is crucial for understanding gene function and regulation.
Current methods may miss coding potential in short or less conserved genomic regions.
Accurate identification of coding sequences aids in expanding genomic databases.

Purpose of the Study:

To develop and validate a novel procedure for detecting coding potential in short genomic sequences.
To identify novel coding potential regions beyond currently annotated genes.
To improve the comprehensiveness of genomic databases with relaxed gene structure assumptions.

Main Methods:

A procedure was developed to assess coding potential in conserved short genomic sequences.
Assumptions on probability models for gene structures were relaxed.
The method was applied to highly conserved human-mouse sequences from the UCSC genome database.

Main Results:

The procedure achieved 91.3% detection of coding potential in known coding exons, covering 83% of human RefSeq coding exons.
A low false positive rate of 2.6% was maintained.
12,688 novel short regions with coding potential were identified at a false discovery rate <0.05, with 65.7% located between annotated genes.

Conclusions:

The developed procedure effectively identifies coding potential in short genomic sequences, including novel regions.
Relaxing traditional gene structure assumptions enhances the discovery of coding DNA.
This method significantly contributes to expanding genomic databases and understanding genome content.