Biotechnology and Bioinformatics (1+1)

B. Sequence search using BLAST

Let us take an example of how to carry out a database search. Assuming that we have a nucleotide sequence named Unknown Sequence#1, and we wish to know whether there are any nucleotide sequences in the database similar to Unknown sequence#1, the search can be performed using the following procedures

7. Access the internet via Internet Explorer or Netscape

8. Type http://www.ncbi.nlm.nih.gov in the location box and press enter

9. From the tools list click on BLAST

10. The main BLAST page appears displaying the d ifferent BLAST programs. Choose blastn for aligning nucleotide sequences

You are now in the NCBI BLAST program. From the top to the bottom, there are a number of blank boxes to be filled in or prechosen as defaults.

Click on the Choose database link to find out information about the databases that can be used in this nucleotide BLAST search. Once a suitable structure database name has been found close the popup window.

11. In the sequence box, type the name of the sequence in the first line. The > must be included immediately before the first letter, otherwise, the database will not recognize the name and treat it as an unknown sequence. The BLAST web pages accept input sequences in three formats; FASTA sequence format, NCBI Accession numbers, or GIs. Start from the second line, type a sequence or paste a sequence cut from another file

 Fig1:   Using the Pull Down Menu to select the BLAST database

Fig2:   Example of a FASTA sequence in the input field

12. Edit the sequence as you wish. Advanced options for the BLAST services are

Expect default Cut-off default

Matrix default Strand both

Filter default Description default

Alignments default

13. Choose to display the results, on screen or by E-mail address. Click Submit Query.

Once the search is complete, the sequence alignments will be exhibited two by two on the screen. Check out the best hits with a description that appears to be correct and closest matching to your sequence.

The results can then be copied or pasted into a regular Microsoft word file. The submitted sequence is called a Query and the aligned sequence from the database is called Sbjct .