UNIT 3.3 Finding Similar Nucleotide Sequences Using Network BLAST Searches

  1. Istvan Ladunga

Published Online: 1 JUN 2009

DOI: 10.1002/0471250953.bi0303s26

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Ladunga, I. 2009. Finding Similar Nucleotide Sequences Using Network BLAST Searches. Current Protocols in Bioinformatics. 26:3.3:3.3.1–3.3.26.

Author Information

  1. University of Nebraska-Lincoln, Lincoln, Nebraska

Publication History

  1. Published Online: 1 JUN 2009
  2. Published Print: JUN 2009


The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge. Curr. Protoc. Bioinform. 26:3.3.1-3.3.26. © 2009 by John Wiley & Sons, Inc.


  • BLAST;
  • sequence alignment;
  • database search;
  • homology search;
  • mapping;
  • nucleic acid;
  • DNA;
  • RNA;
  • genome;
  • blastn;
  • Megablast