Protein Sequence Similarity Search Using pblast Tool

Algorithm:

1.Go to NCBI website (http://www.ncbi.nlm.nih.gov/) and select the Protein database from drop down menu.

2.Enter the Name or Accession id of the query protein sequence.

3.Get the sequence in Fasta format.

4. Now open the Blast tool page using this link (http://blast.ncbi.nlm.nih.gov/Blast.cgi) and select pblast for protein sequence similarity.

5.Paste your query protein sequence in the box provided.

6.Enter the job title and let the parameters default (it can be modified as the per your search requirement).

7.click on the "blast" tab to start database search. 

8. Get the result.

Interpretation:

It will include following things:

Total score:

Maximum score:

It gives the hits in descending order of their similarity.

E-value: 

Essentially, it describes the random background noise that exists for matches between sequences.

It is a parameter that describes the number of hits one can "expect" to see just by chance when searching a database of a particular size. It decreases exponentially with the Score (S) that is assigned to a match between two sequences.

The e-value is used as a convenient way to create a significance threshold for reporting results. When the e-value is increased from the default value of 10, a larger list with more low-scoring hits can be reported. On the other hand, a lower e-value will result in a shorter list with more quality hits.