Basic Applied Bioinformatics

CHAPTER 13Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

13.1 INTRODUCTION

BLASTp is a set of programs that searches the protein databases using an amino acid sequence as the query. There are four different algorithms, with well‐defined applications in BLASTp: blastp, psi‐blast, phi‐blast and delta‐blast.

13.2 OBJECTIVE

To search a homologous protein sequence from the protein database, using the given amino acid sequence as query.

13.3 PROCEDURE

13.3.1 Protein‐protein BLAST (BLASTp)

The necessary steps are the same for BLASTp and BLASTn (see Chapter 12: “Basic Local Alignment Search Tool for nucleotide (BLASTn)”), regarding:

• selection of sequence of interests (query sequences);
• specifying the BLAST program;
• selecting the sequence database;
• adjusting the optional parameters.

13.1.1 Open the BLASTp homepage

Open the URL: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi? PROGRAM = blastp&PAGE_TYPE = BlastSearch&LINK_LOC = blasthome to get the homepage for BLASTp.

BASIC TERMINOLOGIES

1. Position‐Specific Iterative BLAST (PSI‐BLAST): An iterative (repeating the same set of instructions or steps) BLASTp search used for constructing a scoring matrix based on the frequencies of each amino acid in each position (hence, “position‐specific”) of protein sequence alignment (i.e., a profile). The profile is refined with the resulting sequences obtained after each cycle of sequence search. ...