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Use of Alu Element Containing Minigenes to Analyze Circular RNAs

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Using RepeatMasker to identify repetitive elements in genomic sequences.

Maja Tarailo-Graovac¹, Nansheng Chen¹

¹Simon Fraser University, Burnaby, British Columbia, Canada.

Current Protocols in Bioinformatics

|March 11, 2009

Summary

This summary is machine-generated.

This study details how to use RepeatMasker software for identifying repetitive DNA elements in genomes. It provides protocols for web and command-line use, including faster alignment methods for genomic analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Repetitive elements constitute a significant portion of eukaryotic genomes.
Accurate identification and masking of these elements are crucial for genome annotation and analysis.
RepeatMasker is a widely adopted tool for this purpose.

Purpose of the Study:

To provide comprehensive guidelines for utilizing the RepeatMasker software.
To detail methods for analyzing repetitive elements in genomic sequences using RepeatMasker.
To discuss optimizations and best practices for RepeatMasker analysis.

Main Methods:

Description of two Basic Protocols for RepeatMasker usage: Web interface and command-line (Unix/Linux).
Introduction of an Alternate Protocol using WU-BLAST to reduce processing time compared to cross_match.
Discussion of software advantages, limitations, and bug reporting.

Main Results:

Established protocols for effective use of RepeatMasker for repetitive element identification.
Demonstrated methods to optimize analysis speed using alternative alignment programs.
Provided insights into interpreting RepeatMasker output for genomic studies.

Conclusions:

RepeatMasker is an essential tool for repetitive element analysis in genomics.
The described protocols enhance accessibility and efficiency of RepeatMasker usage.
Understanding the software's nuances aids in accurate genome annotation and research.