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Computational Biochemistry for beginners
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Tutorials on how to Conduct homolog and paralog search with NCBI's BLAST sequence alignment & search tools

BLAST means Basic Local Alignment Search Tool. It is a sequence analytical and comparison tool hosted by the National Center for Biotechnology Information (NCBI)



It is used to do a variety of sequence comparison analysis. It can be used for comparing both the protein and nucleotide sequence obtained from the same or different sources

Doing simple sequence comparison search with the NCBI BLAST tool

Before conducting any search with the BLAST tool, its important that you understand specifically the type of information you intend to obtain. Is it homologs, paralogs or just a comparison of a segment of the amino acid or nucleotide sequence?

Homology search is a search that is conducted by comparing your protein (for instance) with the database of all the protein known to man.

Paralog search is when you want to search within the database of a specific organism. For instance, if you want to obtain the set of paralogs of a protein X obtained  from rat, it means that you will configure your search to scan within the database of rats only.

  • Log on to BLAST home page. www.ncbi.nlm.nih.gov/blast/
  • Select Protein BLAST, located under the "Basic BLAST" category (Mouse over the thumbnail fig 1 image to see a larger image)

BLAST home image


Format options of blast
Image of blast query page
Blast home page large image


Blast query page


  • A new page will open up. (FIG 2: mouse over fig 2 to see a more larger image). The page has an input box that will be used used to query the search. The search accepts either the  Pubmed’s accession number of the protein, The FASTA format of the protein (this can be obtained from the NCBI protein database. Copy the whole sequence and paste it in the input text area), a segment of the protein or nucleotide sequence can also be pasted into the input text area.
  • Specify the other options below the input text area, that will suite your purpose, such as the organism’s database that would be compared with your protein.
  • Now click the BLAST button( towards the lower end of the page.)
  • If the page loads well, it will display a page containing the results. You can reformat this result to reduce the numbers of the output results, to change the nature of the file to text or HTML etc: To reformat the result, click the "formatting option" Label of the result page. Mouse over fig 3 to see the formatting options




  • After selecting the formatting option, click the display result button in the same page to display the reformatted result

Consult the site documentation and help for more information on using the BLAST Tool.

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