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RNA-seq

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...

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Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

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PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences.

Satish Chikkagoudar¹, Dennis R Livesay, Usman Roshan

¹Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.

Nucleic Acids Research

|June 5, 2010

Summary

This summary is machine-generated.

This study introduces a new online tool for identifying distant RNA sequence similarities within large genomes using partition function posterior probabilities. The server accurately detects hidden non-coding RNA homologs, aiding genomic research.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Alignment-based programs are crucial for identifying homologous sequences in large genomic datasets.
Partition function posterior probabilities, when applied to local alignment, have demonstrated high accuracy in detecting distantly related non-coding RNA (ncRNA) sequences.
Identifying ncRNA homologs is challenging due to their often-divergent sequences and prevalence within vast genomes.

Purpose of the Study:

To present an accessible online implementation of an alignment algorithm utilizing partition function posterior probabilities for RNA sequence analysis.
To provide a user-friendly server for identifying potential ncRNA homologs within large genome sequences.
To facilitate the discovery of evolutionarily conserved RNA structures hidden in genomic data.

Main Methods:

Development of an online server accepting a query RNA sequence and a large genome sequence as input.
Application of an alignment algorithm based on partition function posterior probabilities attuned to local alignment.
Outputting a ranked list of sequence alignments exceeding a defined mean posterior probability threshold.
Integration with the PLAST alignment viewer applet for visualization of high-probability alignment regions.

Main Results:

The server successfully identifies potential RNA sequence homologs in large genomes.
The output format is optimized for local alignment viewing.
High posterior probability regions within local alignments are highlighted for detailed inspection.
The tool provides a valuable resource for comparative genomics and ncRNA discovery.

Conclusions:

The developed online server offers an accurate and efficient method for discovering distantly related ncRNA sequences in large genomes.
This tool enhances the capability to find functionally important RNA elements that might otherwise be missed.
The freely available web server democratizes access to advanced RNA sequence analysis techniques for the research community.