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NCBI BLAST Database Searching

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Prerequisite Terminologies

In order to have thorough understanding of the main topic, you should have the basic concept of the following terms:

Primary Biological Sequences.
Python and R.
FASTA format.
[watch our video on FASTA format]
Non-redundant (nr/nt) database.




Hamsa Ehsan


In bioinformatics, Basic Local Alignment Search Tool (BLAST) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. Query is searched against the entire database of GenBank or the entire datasets which have been incorporated in NCBI.


  • You can access BLAST whether from web-browser, or through installing the command line BLAST to your computer or through programming languages such as Python and R.

  • Go to the BLAST web-browser.

  • Here you will see four kind of Blast which you can use.     

BLAST Type                                          Query Type                                         Database type

Nucleotide BLAST                             Nucleotide                                        Nucleotide

Protein BLAST                                     Protein                                               Protein

BLASTX                                                Translated Nucleotide                    Protein

TBLASTN                                             Protein                                               Translated Nucleotide

Nucleotide BLAST

  • A page will be opened, where you can customize your search according to your analysis.

  • In the ‘Enter Query Search’ box, you can put accession number or copy the FASTA sequence of your nucleotide query.

  • Beside this box, you can see ‘Query subrange’ box, from where you can subset your query and tell from what nucleotide to what nucleotide you want to search.

  • You can also upload the sequence file from your computer.

  • In ‘Job Title’, you can give a descriptive title for your BLAST search.

  • In ‘Database’, you can select any kind of database you want to search against; For nucleotide sequences, non-redundant (nr/nt) database is a good option.

  • In ‘Organism’ (which is optional), you can select the organism or organisms you want to search against or you can exclude those organisms from your search.

  • All of the next parameters are optional, which won’t matter until you want to include them according to your own analysis.

  • In ‘Program Selection’ section, you can select the option which is better for your own analysis.

  • Click on the ‘BLAST’.

  • The BLAST analysis will be opened, where you can analyze your query with many other aligned nucleotide sequences.


  • From Blast web-browser, go to ‘tblastn’.

  • Put in the accession number or FASTA sequence in the query box.

  • Select nucleotide non-redundant(nr/nt) database from the ‘Database’.

  • BLAST it.

  • The analysis page is same as any other kind of BLAST (for example Nucleotide Blast).

  • You can analyze your query with aligned mRNA sequences.

  • You can see that ‘Percentage Identity’ is lower as compared to Nucleotide BLAST, it’s because of Codon Degeneracy.

  • You can also visualize your sequences in many kinds of alignments.


In this video, we learnt about BLAST and how we can use it to compare different biological sequences to different databases.

File(s) Section

If a particular file is required for this video, and was discussed in the lecture, you can download it by clicking the button below.

Useful Data
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