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Related Experiment Video

Updated: Jun 22, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Finding similar nucleotide sequences using network BLAST searches.

Istvan Ladunga¹

¹University of Nebraska-Lincoln, Lincoln, Nebraska.

Current Protocols in Bioinformatics

|June 5, 2009

Summary

This summary is machine-generated.

This guide teaches beginners how to use the Basic Local Alignment Search Tool (BLAST) for sequence analysis. Learn to perform BLAST searches and interpret results for genomic mapping and gene discovery.

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The ITS2 Database

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The Basic Local Alignment Search Tool (BLAST) is fundamental in bioinformatics.
Its performance and user-friendliness make it essential for sequence analysis.

Purpose of the Study:

To provide a guide for beginner and intermediate users on designing and submitting BLAST searches.
To explain how to interpret BLAST results for biological significance.

Main Methods:

Utilizing the National Center for Biotechnology Information (NCBI) web pages for blastn and Megablast searches.
Mapping nucleic acid sequences to genomes and identifying similar sequences (mRNA, EST, ncRNA).
Employing translated BLAST for homologous protein identification and low-complexity region filtering to reduce false positives.

Main Results:

Megablast searches are significantly faster than blastn.
Results interpretation is aided by taxonomy reports, genomic views, and multiple alignments.
Parsed BLAST results can be integrated into analysis pipelines for further study.

Conclusions:

BLAST is a powerful tool for sequence similarity searching and gene discovery.
Understanding significance thresholds and utilizing integrated databases enhances biological knowledge discovery.
BLAST facilitates integration with a wide spectrum of biological information.