Learn to use BLAST, (Basic Local Alignment and Search Tool), the sequence similarity searching tool from the National Center for Biotechnology Information (NCBI) at NIH. You can use BLAST to find sequences similar to your nucleotide or protein sequences. There are also a variety of specialized BLAST programs available, including Primer-BLAST, VecScreen, SNP BLAST options, multiple alignment tools, and more. You can easily compare 2 sequences to each other. These can provide invaluable information in your quest to infer functional and taxonomic relationships for known or unknown sequences, or to further design experiments.

You will learn:

  • how to do basic nucleotide and protein BLAST searches
  • how to interpret and save your BLAST results
  • how to manipulate your data for easy analysis and visualization
  • to customize and save your searches and results with My NCBI
  • to use some of the specialized BLAST tools for multiple alignments and SNP analysis


This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:

ClustalW2: Performs multiple sequence alignments

FASTA: FASTA sequence algorithm

Entrez Gene: NCBI's Entrez tool for gene-centric information

Primer3: Pick primers from a DNA sequence.

DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools

VISTA: Tools for Comparative Genomics

RefSeq: Provides molecular sequence records to help locate gene and protein data.


Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).


Friday SNPpets: This week's SNPpets include a range of things, from Pardis Sabeti's recovery from a serious accident to tardigrade genome drama. There are new databases and tools such as the GMO sequence tracker in th...

Friday SNPpets: This week's SNPpets offered a lot of good stuff, everybody must be out of their summer vacation mode and back to the lab. There's a BLASTX alternative, a helpful tip in workshop teaching, quack DTC tes...

Bioinformatics tools extracted from a typical mammalian genome project [supplement]: This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to ...

Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...

Video Tip of the Week: Sharing #H7N9 data at GISAID.org with EpiFlu™: This week’s video Tip of the Week offers you a quick tour of GISAID’s resources and their EpiFlu™ database. This is the database you might be hearing about in the news—the one to which researchers sub...


Recent BioMed Central research articles citing this resource

Mosquera-Rendón Jeanneth et al., Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2364-4

Fan Chao et al., PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0851-2

Watson M. Christopher et al., Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping Clinical-Molecular Genetics and Cytogenetics. BMC Medical Genetics (2016) doi:10.1186/s12881-015-0265-z

Melo T. O. Arthur et al., GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data Sequence analysis (methods. BMC Bioinformatics (2016) doi:10.1186/s12859-016-0879-y

Tatarinova V. Tatiana et al., The mysterious orphans of Mycoplasmataceae. Biology Direct (2016) doi:10.1186/s13062-015-0104-3